The reform and deepening of the rural collective property rights system play a crucial role in promoting rural household income growth and advancing the goal of common prosperity. This paper constructs a theoretical framework of “three changes” reform-factor allocation-rural household income. Using panel data from 220 prefecture-level cities in China from 2005 to 2021, the Synthetic Control Method (SCM) is employed to quantitatively assess the impact and effects of the “three changes” reform on rural household income. The Propensity Score Matching Difference-in-Differences (PSM-DID) model and the mediating effect model are applied to test the robustness of the results and analyze the underlying mechanisms. The key findings are as follows: 1) The “three changes” reform has significantly increased the per capita disposable income of rural residents; 2) It enhances rural household income by optimizing the allocation of land resources between regional characteristic industries and traditional industries, as well as by improving the allocation of capital factors among different agricultural business entities; 3) The reform promotes income growth by influencing rural labor allocation and increasing wage-based earnings. Based on these findings, future efforts should focus on standardizing reform practices, refining the assessment of key implementation stages, and improving the evaluation of reform outcomes to ensure policy effectiveness. Additionally, advancing the establishment of service platforms for land, capital, and labor, optimizing the macro-level reform environment, and developing supporting mechanisms are essential to the successful implementation of the “three changes” reform.