The Rural Collective Land Joint-stock Cooperative System (RCLJCS) is a new measure to strengthen rural collective economy and increase rural household income. Based on a field survey data of 1051 farmers of Meixian of Shaanxi Province, this paper analyzed the impacts of the RCLJCS reform on farmers’ income and the difference of its impacts on farmers’ income with different production efficiency by the PSM-DID model and explored the mechanism of income growth effect by the mediating effect model. Results show that the collective land management mode was dominated by the internal and external share leasing. The scale management effect was remarkable, and the share dividend ratio reached 45.45%. The reform of the RCLJCS has shown initial results and had different effects on farming income and wage income of rural households with a significant positive impact on the total household income, which could effectively increase the income by 17 290 yuan. At the same time, the reform of the RCLJCS had a stock incentive effect, an industrial driving effect, and a labor transfer effect, forming a stable transmission mechanism for the increase of rural households’ income. In addition, based on different mechanisms of action, the RCLJCS had differential impacts on rural household income with different production efficiency. The increase in farming income of high-efficiency farmers was more obvious, and the increase in wage income of low-efficiency farmers was more significant. Therefore, to serve the development of agricultural modernization and rural revitalization strategy, this paper suggests to actively promote the reform of the RCLJCS, to implement differentiated technical means of the land joint-stock cooperative system, and to improve the relevant management and service of land joint-stock reform.