Currently, China is in a strategically critical period for cultivating new quality productive forces. The demand for long-term, stable, and risk-tolerant funding for innovation activities is particularly urgent, making patient capital a key force in addressing the financing challenges of innovation. Since the concept of patient capital emerged in the policy landscape, scholarly attention to its economic consequences has grown, yet there remains a lack of in-depth exploration into its relationship with innovation strategy choices. Independent innovation and collaborative innovation differ significantly in terms of resource requirements, risk-taking, and value creation, and therefore, the impact of patient capital on these two innovation strategies should also differ. Investigating the influence of patient capital on firms’ innovation strategy choices can provide insights for resolving innovation financing difficulties and optimizing the allocation of innovation resources, holding significant theoretical and practical importance. Against this backdrop, this study systematically investigates how patient capital influences firms’ strategic choice between collaborative and independent innovation. To capture this strategic preference, the variable of independent innovation bias is introduced, which measures the extent to which firms favor independent innovation over collaborative approaches. The study then examines the effect of patient capital on firms’ independent innovation bias. Furthermore, the moderating roles of market competition and slack resources, as well as the mediating mechanisms of R&D investment and human capital, are tested. Using panel data of Chinese listed companies from 2009 to 2023, sourced from the China Research Data Services Platform (CNRDS) and the CSMAR database, this study empirically tests the proposed theoretical model. To ensure the robustness of the findings, multiple tests are conducted, including instrumental variable estimation, alternative regression methods, re-measurement of key variables, and sample size adjustments. The results remain consistent with the baseline regression. Empirical results indicate that patient capital promotes a firm’s independent innovation tendencies. When market competition is intense, the positive relationship between patient capital and independent innovation bias is more pronounced; conversely, when firms have abundant slack resources, this relationship is weakened. Mechanism analysis reveals that patient capital enhances independent innovation bias by increasing human capital and R&D investment. Further analysis shows that independent innovation bias helps strengthen firms’ total factor productivity and enhances their financial performance and market value. By systematically exploring the mechanisms through which patient capital affects independent innovation bias, this study refines the research on the economic consequences of patient capital by shifting the focus from innovation output to strategic choice. It also expands the research on factors influencing innovation strategies by introducing the perspective of capital attributes, thereby enriching the relevant research on patient capital and innovation strategy choice. The findings provide empirical evidence for firms to align their innovation strategies with capital time horizons and for governments to improve the institutional supply of patient capital. Moreover, they offer policy insights for accelerating the cultivation of new quality productive forces and achieving high-level technological self-reliance.