Improving the efficiency of green development is an important means of achieving high-quality development, and the optimal allocation of financial resources is the core factor in promoting green development. Based on the panel data of 30 provinces in China taken from 2005 to 2021, this paper constructs a financial resource misallocation (FM) index and green development efficiency (GDE) measurement system, empirically examining the impact and transmission path of FM on the GDE from the dual perspectives of financial resource element mismatch and structural mismatch. First, the results show that financial misallocation is the key factor inhibiting the improvement of GDE, and with the improvement of GDE, the inhibitory effect of financial misallocation decreases first and then increases in an inverted V-shaped trend. Second, the inhibitory effect of financial resource structure mismatch on GDE is greater than that of financial resource element mismatch. Moreover, after the degree of financial marketization is distinguished, this inhibitory effect is more evident in the regions with a low degree of financial marketization. Third, through mechanism analysis, we found that FM affects the improvement of GDE by inhibiting financial resource agglomeration through enterprise technological innovation and industrial structure height.