The management of economic growth goals is one of the important means for the Chinese government to drive economic development. The setting and realization of local economic growth goals will have an important impact on regional economic development and micro-enterprises’ behavior. Under the extensive economic development mode that mainly pursues quantitative growth, GDP growth rate has become the core indicator of local government performance evaluation, and a pattern of local governments “competing for growth” has been formed. In this case, the excessively high local economic growth target setting and the hard constraint of achieving the target lead to the local government’s excessive intervention in the regional economy to ensure the realization of the target, and this intervention will inhibit the growth of enterprise R&D investment. An analysis of A-share listed companies in China’s Shanghai and Shenzhen stock exchanges from 2007 to 2018 found that the higher the local economic growth target is, the lower the R&D investment intensity is; too high local economic growth target will lead to the expansion of regional infrastructure construction, industrial structure inclining towards industrialization and relatively slow development of technology market, and drive enterprises to increase physical capital investment, increase leverage ratio and reduce financial stability, all of which will have a negative impact on enterprise R&D investment. Further research finds that the change of local government behavior will lead to the change in the relationship between “local economic growth target and enterprise R&D investment”. The “overweight” behavior of local governments on economic growth targets (exceeding national and regional targets) and the increased assessment pressure brought by the approach of the “Five-Year Plan” assessment will strengthen the negative relationship between the local economic growth targets and enterprise R&D investment. In the local government competition system, the relative weakening of “competition for growth” and the relative strengthening of “competition for innovation” can effectively improve the structural mismatch of local economic growth target and enterprise R&D investment”. The transformation of the economic development mode has brought about the structural adjustment of the local economic growth target, and effectively weakened the negative relationship between “the local economic growth target and enterprise R&D innovation”. Therefore, it is necessary to deepen the reform of the local government performance appraisal system and optimize the structure of the local government competition system. Governments at all levels should pay attention to the possible negative effects of setting too high economic growth targets and prudently set short-term economic growth targets. Local governments should effectively transform the mode of economic development, improve the fit between the management of economic growth targets and the innovation and development of enterprises, and clear the obstacles that hinder enterprise innovation activities.