With the rapid development of renewable energy, small hydropower station, as a kind of clean energy, shows a good development prospect. However, at present, small hydropower stations are faced with problems such as small scale, insufficient mechanism of participating in power grid dispatching and urgent innovation of operation mode of peak and frequency regulation. Based on the operation characteristics of small hydropower station, considering the cost and emission of thermal power units and the stable operation of small hydropower station, a small hydropower station model with multi-level gradient variable speed water control and stability regulation is constructed. At the same time, an improved growth rime algorithm and multi-gradient supply-storage cooperative scheduling strategy are proposed to explore the optimal decision scheme to realize the economic benefit, environmental benefit and scheduling stability of the system. The experimental results show that compared with other algorithms such as particle swarm optimization (PSO), grey wolf optimizer (GWO) and crested porcupine optimizer (CPO), The improved rime optimization algorithm can improve the economy of the system by 8.7%, reduce the pollution emission by 20.6%, and enhance the operation stability of the small hydropower station by 32.6%. The results validate the effectiveness of the proposed model and algorithm, and provide a new idea for the coordinated operation optimization of multi-source energy complementary systems.