It is of great significance to clarify the evolutionary features of ecosystem services (ES), which not only provides policy-making basis for the improvement of ecosystem services, but also helps maintain and enhance human well-being as well as leads to the sustainable urban development. In this study, we developed a new approach to cluster the spatiotemporal change trajectories of ecosystem services based on ecosystem service bundles. Taking Shenzhen City as an example, we determined the ES bundles at sub-district level based on the combination of 11 selected ecosystem services, and then explored the spatiotemporal evolution of ecosystem services in long time series. From 1980 to 2015, there were six ecosystem service bundles. The spatial distribution of the six kinds of ecological service bundles had little change, and the changing areas were mainly adjacent to Hong Kong. In addition, eight evolution trajectories were identified, most of which were stable in long-term. Furthermore, the spatiotemporal evolution of ecosystem services is consistent with urban expansion to some extent, which indicates that urban expansion may determine the structure and function of urban ecosystem.