This paper constructs a theoretical model to explore the mechanism of factors input changes caused by agricultural population transfer affecting rural industrial structure，and makes an empirical test using 2001-2013 the agricultural sub-sector data from 216 cities in China.The study found that：（1）Rural labor transfer has a significant inhibitory effect on crop production，but the effect of the alternative labor of capital has a significant positive impact on agriculture，forestry，animal husbandry and fishery services；（2）The transfer of agricultural population has significantly increased the capital-labor ratio of the agricultural sector and promoted rural production.The transformation and upgrading of industrial structure and the upgrading of professional service level，but the deterioration of human capital tends to have a greater negative impact；（3）The change of relative labor costs caused by the transfer of agricultural population has a greater impact on the eastern region，and the rural industrial structure in the central and western regions is more significantly constrained by human capital.The transformation and upgrading of rural industries that pays attention to the return of human capital has important policy implications for realizing the strategy of rural rejuvenation.