Based on the construction of the evaluation index system for the supply efficiency of water ecological products in Zhoushan City, the evolutionary characteristics of the supply efficiency of water ecological products in Zhoushan City from 2000 to 2017 were analyzed by using the RSBM-DEA model based on time series data, and the influencing factors were analyzed. The results show that the value of water ecological services in Zhoushan City is mainly reflected in surface water storage and cultural services, showing a fluctuating upward trend. The supporting effect of water ecosystem on the sustainable development of Zhoushan's economy and society has been continuously enhanced. The supply efficiency of aquatic ecological products in Zhoushan City has maintained a fluctuating development trend at a high level, of which pure technical efficiency is the key factor. In 2003 and 2013, it experienced two “trough periods”, mainly caused by the impact of pure technical efficiency. Different factors have different influence directions and degrees on the supply efficiency of water ecological products in Zhoushan City. Among them, the level of science and technology, the construction of water conservancy facilities, industrial structure and the level of economic development have a very significant positive impact, while the annual average temperature and ground hardening rate have a negative impact on the ground hardening rate, and the ground hardening rate has a low impact.