The balance of man-land relationships is at the heart of national park construction, and alleviating spatial conflicts is key to achieving man-land coexistence in national parks. In this paper, based on the 2020 sampling survey and ecological monitoring data, we use the coupling degree model, the barrier degree model, and the regression model to measure the level of spatial conflict in the man-land system and explore its mechanisms of action. The study shows that: (1) The spatial conflict in the man-land system of Three-River-Resource National Park is apparent, and the coupling coordination degree of 98.11% of 53 administrative villages belongs to the type of near disorder and mild disorder. (2) From the perspective of internal action mechanism, the severe obstacle factors of spatial conflict of the man-land system have green development mode and soil-water resources conservation, the moderate obstacle factors have the ability of asset accumulation ability, competition and cooperation ability, and the ability to continue to increase income, and the mild obstacle factors have the ability of health security. (3) From the perspective of external direct action mechanisms, the government’s ecological governance capacity and the degree of resource dependence have a significant effect on the spatial conflict of the man-land system, and the per capita disposable income has significantly aggravated the conflict. (4) From the perspective of external indirect action mechanism, environmental pressure has a significant regulatory effect on the government’s ecological governance ability and the spatial conflict between the man-land system, and the intensity of economic activity has a significant intermediary effect on the relationship between resource dependence and the spatial conflict of man-land system.