Based on the provincial panel data of China from 2002 to 2015, the impact of environmental pollution on regional innovation level is studied. Human capital is used as a mediator variable to study the transmission mechanism using mediating effects. It finds that environmental pollution reduces China's innovation level significantly. human capital is an important transmission channel for environmental pollution to affect the level of innovation. Environmental pollution will have a negative impact on the level of innovation by reducing the level of human capital. The enlightenment of this paper is: The government should strengthen the control of environmental pollution and increase the human capital investment to create good conditions for human capital accumulation and agglomeration. Besides, transportation infrastructure should be strengthened continually and R&D investment should be appropriately increased so as to provide a good foundation for the improvement of innovation level.