Abstract: Clarifying the carbon-reducing and sink-enhancing effects of rural industrial integration and optimizing the pathways for agricultural and rural carbon emission reduction and carbon sequestration has important theoretical and practical significance for the green transformation of agriculture. Based on panel data from 13 prefectures and cities in the Xinjiang from 2007 to 2022, this study analyzed the spatiotemporal evolution of rural industrial integration, agricultural carbon emissions, and carbon sinks, and examined the impact of rural industrial integration on agricultural carbon reduction and sink enhancement through a two-way fixed effects panel model. The study found that: 1) the development trends of rural industrial integration and total agricultural carbon sinks were similar, both experiencing three stages: ‘fluctuating or slow growth, rapid decline, and rapid or slow growth’. The agricultural carbon emissions has gone through two stages: slow growth, and rapid decline-stabilization. The spatial distribution of rural industrial integration was characterized by higher levels in the central and eastern regions and lower levels in the western part of the study area, exhibiting significant spatial agglomeration characteristics, which were mainly manifested in the two patterns of ‘high-high’ and ‘low-low’ agglomerations. Areas with high agricultural carbon emissions and sinks were mainly concentrated in the border port economic zone. The Ili Kazakh Autonomous Prefecture experienced a misalignment of agricultural carbon emissions and carbon sinks during the study period. 2) Rural industrial integration had a positive impact on agricultural carbon reduction and sink enhancement, resulting in a reduction in agricultural carbon emissions of 0.049%–0.052% and an increase in agricultural carbon sinks of 0.060%–0.090%, a conclusion that still held after robustness and endogeneity tests. 3) Mechanism analysis indicated that rural industrial integration realized agricultural carbon reduction and sink enhancement by releasing “technology dividends” and “factor dividends” to drive green technological change and optimize factor allocation. Specifically, rural industrial integration reduced agricultural carbon emissions by promoting green technological innovation and large-scale land management, while enhancing carbon sinks through technological progress and rural human capital development. Accordingly, a regionally-adapted industrial integration model was recommended, emphasizing the “water-carbon” synergy and a “green technology-human capital” dual-wheel drive to address spatial development imbalances and innovate the industrial integration pathway in arid areas, thereby accelerating the realization of agricultural emission reduction, carbon sequestration, and the high-quality development of agricultural economy.