For a long time, theory of anti-corruption by regulations, market and culture has no thoroughly focus and system design on material motivation behind grassroots corruption. The interest theory of Marxism can make up for the insufficient. Interest is the way of explanation for grassroots corruption, and interest regulation is the system logic of governance of grassroots corruption. By analyzing the formation factor and anti-corruption motivation generation of grassroots corruption under the perspective of interest theory, the benefit structure, internal mechanism and basic rule of grassroots corruption governance can be deeply understood, and then governance path of grassroots corruption under the background of modernization of national governance system can be explored. Entering the new era, only by cleaning up boundary of powers and functions of the four main bodies of grassroots Party organizations, grassroots administrative organs, market subjects and grassroots people around interest regulation, and by perfecting the four elements of anti-corruption of knowledge premise, systems and mechanisms, the rule of law and regulations, and reporting channels, can the soil of grassroots corruption be effectively eradicated.