Against the backdrop of the “storing grain in land and technology” strategy and pressing food security challenges, understanding biased technological progress in grain production is crucial. This study constructs a three-factor Constant Elasticity of Substitution (CES) production function—incorporating agricultural machinery, chemical fertilizer, and labor—and employs a normalized supply-side system with Nonlinear Seemingly Unrelated Regression (NLSUR) to analyze biased technological progress across 26 Chinese grain-producing provinces from 2004 to 2023. Total factor productivity (TFP) is also decomposed to assess this progress’s contribution. The results indicate that first, technological progress generally evolves along a “machinery–fertilizer–labor” path. Recently, the primary driver shifted from machinery to fertilizers, aligning with fertilizer reduction and green development policies. Second, TFP growth exhibits phased characteristics, declining during the post-agricultural tax reform period (2005–2013) and rising amid supply-side structural reforms and the “storing grain in technology” strategy (2014–2023). Third, marketization, demand, and digitalization promote fertilizer-oriented progress; specialization drives machinery-oriented progress; and road infrastructure facilitates labor-oriented progress. These results offer empirical evidence for policy evaluation and guidance for optimizing factor allocation, advancing the green transition, and safeguarding food security.