To address the growing demand for energy conservation and environmental protection in rail transit, coupled with the persistent reliance on diesel traction in certain regions, this paper proposes a hybrid power transmission system designed for compact under-floor installation in electric multiple units (EMUs), along with a dedicated hybrid gearbox as its core component. A system simulation model was developed, with emphasis placed on comprehensive efficiency optimization via backward simulation, through which the optimal operating mod and power distribution strategies under various speed and acceleration conditions were identified. A prototype system—comprising an under-slung hybrid power pack and a roof-mounted battery pack—was manufactured and validated using a custom test bench. The findings provide a systematic technical pathway and theoretical foundation for the hybridization of EMUs.