Ecosystem services are the basis of human survival and development. Assessment of urban ecosystem services and zoning of ecological management units can contribute to the improvement of living environment. Based on the functional characteristics of ecosystem services in highly urbanized areas, this paper used ecosystem service value equivalent to calculate ecosystem service value of different land types. The ecosystem service index system was constructed from two aspects of ecological function and economic function, and the ecosystem service value of 666 community units was evaluated in Shenzhen, 2017. Using spatial autocorrelation analysis method, according to the combination types generated by the locally spatial agglomeration characteristics, different community ecological management units were divided, and ecological zoning control strategies were put forward. The results show that: 1) ecosystem service value assessment is convenient for the overall evaluation of urban ecosystem service function in highly urbanized areas. 2) The spatial difference of ecosystem service value was obvious in Shenzhen in 2017, showing the spatial pattern of high in the east and low in the central and western regions. The total value of ecosystem service in Shenzhen was about 58.396 billion yuan, the highest value was 16.025 billion yuan in Dapeng New District, and the lowest value was 1.324 billion yuan in Futian District. 3) The 666 community units were divided into 4 kinds of urban ecological management zones, and the differentiated zoning control measures were adopted, which shows that the effective urban ecological management zones can take into account the various ecosystem service functions and realize the optimization of the functional benefits. The results of this study are valuable for the scientific management of regional ecosystem services and the differentiated management of ecological governance.