Based on the 30 provincial data of China from 2005 to 2017, the super-efficient SBM model was used to measure the inter-provincial agricultural eco-efficiency, and a panel threshold model with rural labor transfer as the threshold variable was established to investigate the impact of rural population aging on agricultural eco-efficiency. Non-linear effects, and the effect mechanism and sub-regional tests were carried out. The results show that: ①The aging of the rural population has a negative effect on agricultural ecological efficiency as a whole. This negative correlation decreases with the change of the labor transfer stage, and gradually tends to be insignificant, and finally increases; ②In the test of the promotion and reduction effect mechanism of rural population aging on agricultural ecological efficiency, 13.60% is caused by the mediating effect of the reduction of land size, and 24.63% is caused by the decline of rural human capital. The increase in the level of mechanization can offset part (55.56%) of the negative effect of rural population aging on agricultural ecological efficiency; ③When the rural labor transfer in the eastern region is less than 64.45%, the negative impact of the aging of the rural population on agricultural ecological efficiency has not yet manifested, the central region also shows a negative correlation, and this negative effect increases firstly and then decreases; the negative effect in the western region shows a gradual decrease trend before crossing the third threshold; After the northeast region cross the threshold of 42.11%, the negative effect of rural population aging on agricultural ecological efficiency has increased.