The organic embedding of CPC organization in the corporate governance system through two-way entry and cross-appointment is a unique institutional arrangement in China, and it is also an important starting point for a new round of enterprise reform. The existing literature shows that the embedding of CPC organizations has effectively improved the corporate governance and business performance of enterprises, but there is insufficient research on whether the embedding of CPC organization can improve the relationship between enterprises and other economic entities, especially the lack of relevant empirical evidence. This paper argues that the embedding of CPC organizations can effectively reduce the operational risks and major misstatement risks of enterprises by improving corporate governance. The operational risk and major misstatement risk of the audited unit are important factors that determine the auditor’s decision-making, so there will be a clear correlation between the embedding of CPC organization in the audited enterprise and the decision-making of the auditor, and the strength of this correlation is related to the degree of the improvement effect of the corporate governance brought by the embedding of CPC organization. When the initial corporate governance level of the enterprise is low (such as poor internal control quality), the corporate governance improvement effect of CPC organization embeddedness is greater, so the correlation between CPC organization embeddedness and auditors’ decision-making is also strong. When the Party building work of the grassroots Party organization of the enterprise is strengthened, the improvement effect of corporate governance brought by the embedding of CPC organization will increase, so the correlation between CPC organization embeddedness and auditor decision-making will also be enhanced. This paper takes A-share listed companies in Shanghai and Shenzhen stock exchanges from 2010 to 2019 as samples to examine the relationship between CPC organization embeddedness (two-way entry and cross-appointment) and auditor decision-making (audit opinion and audit fees). The study found that the embeddedness of CPC organization in the audited enterprises is significantly negatively correlated with the probability of the auditors issuing non-standard audit opinions and audit fees, and the internal control quality of the audited enterprises negatively regulates this negative correlation (the improvement of the internal control quality will weaken the negative correlation), and this negative correlation is more significant after the 18th National Congress of the Communist Party of China than before. It can be seen that the embedding of CPC organizations must effectively improve corporate governance and reduce the operational risks and major misstatement risks of enterprises, so as to increase the probability of auditors issuing standard audit opinions, and reduce audit fees. The embedding of CPC organizations will not only improve the efficiency of enterprises, but also improve the relationship between enterprises and other economic entities, reduce the transaction cost of market operation, thus promoting the welfare and efficiency of the whole society. Compared with the existing literature, this paper attempts to explore the positive impact of CPC organization embedding from the perspective of the relationship between enterprises and other economic entities, expands the research on the economic effects of CPC organization embedding, and also deepens the research on the influencing factors and mechanisms of auditor decision-making. Through the analysis of the relationship between the embedding of CPC organization in audited enterprises and the decision-making of auditors, this paper reveals that CPC organization embedding can reduce transaction costs between enterprises and accounting firms by improving corporate governance and transmitting positive signals, which is conducive to deepening the understanding of the overall effect of CPC organization embedding, and providing experience reference and policy enlightenment for further improving the embedding mechanism of CPC organization in enterprises and strengthening the construction of grass-roots party organizations in enterprises.