Xinjiang is a representative dry area in China characterized by oasis agriculture. In recent decades, the amount of farmland has increased considerably. For the regional objectives of “carbon peaking and carbon neutrality”, it is essential to investigate the carbon effects induced by large-scale changes in farmland. This research integrates the PLUS and InVEST models to calculate the carbon effects resulting from the spatiotemporal changes in farmland distribution in Xinjiang. It quantitatively assesses the changes in land-use patterns and carbon storage under four scenarios for 2035—natural development (ND), economic development (ED), ecological protection (EP), and farmland protection (FP)—and explores the spatial agglomeration degree of the carbon effect of cultivated land area change. The analysis reveals the following: (1) From 1990 to 2020, the farmland area in Xinjiang showed a trend of first decreasing and then increasing, resulting in a total increase of 33,328.53 km2 over the 30-year period. The newly added farmland primarily came from grassland and unused land. (2) The terrestrial ecosystem carbon storage in Xinjiang showed a trend of decreasing first and then increasing, with an increase of 57.49 Tg in 30 years. The centroid of carbon storage was located in the northwestern part of the Bayingolin Mongol Autonomous Prefecture, showing an overall southwestward shift. Changes in farmland area contributed to a regional carbon storage increase of 45.03 Tg. The contribution of farmland to carbon storage increased by 3.42%. (3) In 2035, the carbon storage value of different scenarios will increase compared with 2020, and the carbon sink of cultivated land will be the maximum under the cultivated land protection scenario. (4) There is a strong spatial positive correlation between the changes in carbon storage caused by the change in cultivated land area in Xinjiang, and there are more hot spots than cold spots. The carbon storage changes under farmland transformation have the characteristics of “high-high” clustering and “low-low” clustering. Future territorial spatial planning in Xinjiang should comprehensively coordinate ecological protection and farmland conservation measures, improve regional carbon sink capacity, and achieve green and sustainable development.