Inner Mongolia Autonomous Region (IMAR) has become the sixth-largest grain-producing province of China, contributing 5.6% of the total national grain output in 2021. Grain production increased by around 821% from 1980 to 2019. The contributions of structure adjustment, sown area, and yield to the increase in grain production was analyzed for IMAR. For yield, the Cobb–Douglas production function was estimated, to analyze the contribution of agricultural inputs (fertilizer, irrigation, seed, pesticide, agriculture film, and machinery operation) and the impact of natural hazards on yield. Results from our study showed that the grain production and yield in IMAR increased by 81.40 × 104 t and 0.11 t·ha−1 annually from 1980 to 2019. The grain-crop sown area increased by 73.65 × 103 ha annually, and the sown area of maize constitutes 16.82% to 55.30% of the total sown area of the IMAR in 1980–2019. In IMAR, sown area, yield, and structure adjustment can explain 54.06%, 33.31%, and 12.63% of the increase in the total grain production, respectively, from 1980 to 2019. The input per unit area of fertilizer, irrigation, and other inputs (seed, pesticide, agricultural film, and mechanical operation inputs) increased by 362.16%, 259.66%, and 405.55%, respectively, from 1981 to 2019, which contributed 160.44%, 15.06%, and 53.13% for the main cereal grain (maize and wheat) yield, respectively, while the decrease in the comprehensive loss rate from agrometeorological hazards contributed 7.76% to the main cereal grain yield in IMAR. Technologies such as water-saving irrigation, high-efficiency fertilizer application, and agrometeorological-hazards mitigation measures should be adopted in the future to increase production, considering the stable sown area and environmental and resource constraints.