Driven by the dual objectives of agricultural green transition and carbon neutrality, new energy agricultural machinery has emerged as a pivotal solution to replace traditional fuel-powered equipment while enhancing energy efficiency in farming. This study investigates powertrain systems for new energy agricultural machinery, analyzing design characteristics of mainstream technologies, including pure electric, hybrid, and clean fuel systems. Through critical design phases such as core component matching, drive configuration optimization, and energy management strategy formulation, the research proposes multidimensional energy efficiency enhancement methods tailored to operational conditions. Experimental validation confirms the feasibility and efficiency improvements of proposed designs. Results demonstrate that optimized powertrain systems with intelligent energy management can reduce energy consumption by 15–25% and increase operational efficiency by over 10% during typical tasks like plowing, rotary tilling, and transportation. Addressing existing challenges such as inadequate core technology compatibility and efficiency bottlenecks, the study offers technical breakthrough recommendations and industrial development strategies, providing theoretical references and practical pathways for advancing new energy agricultural machinery research and promotion.