Improving the efficiency of factor allocation in food production is the foundation for accelerating the formation of new quality productivity and achieving an agricultural green transformation. However, there has been no scholarly focus on their mechanisms and the interactions involved. This exploration is an important reference for enhancing the green production capacity of major grain-producing areas. In this study, 13 prefecture-level cities in Heilongjiang Province, China’s largest grain production base, were selected as the research samples. A model for identifying factor misallocation and grain green total factor productivity (AGGTFP) was constructed to identify the spatiotemporal differences in factor misallocation and green total factor productivity. A fixed effects model was used to explore the impact of single-factor misallocation and the interaction of dual-factor misallocation with AGGTFP. The results show that from 2004 to 2022, the AGGTFP in 13 prefecture-level cities in Heilongjiang Province has shown a slow growth trend. The inhibitory effects of single-factor misallocation of land, labor, and capital on green total factor productivity are sequentially enhanced. The interaction effects of capital misallocation and labor misallocation and labor misallocation and land misallocation strengthen the inhibitory effects of misallocation on the AGGTFP. Therefore, it is necessary to further promote the optimization of production factors and improve the green production capacity for grain.