The contradiction between the contribution of city logistics (CL) to sustainable urban development and its negative externalities is increasingly prominent. Policy supervision measures and the green logistics initiative are also in conflict with the management goal of logistics enterprises. Innovative solutions for CL have attracted increasing research attention worldwide. However, the description of the global research network in the field of CL, research trends, and the discussion of advanced theories and practices have not been systematically reviewed so far. Especially in the past three years, there has been an explosive growth of relevant literature. In this paper, the method of combining scientometric analysis and thematic discussion was adopted to systematically review 513 important works in the literature from 1993 to 2018, aiming to provide a holistic understanding of the status in quo, trends and gaps of CL research, and to further analyze prominent problems. The study has made statistical analyses of the publication year profile, journal allocation and research methods of the included literature, and constructed four kinds of visualized bibliographic information timeline maps for the authorship network, international collaboration network, keywords co-occurrence network and research topic clustering. Then, the three themes summarized by clustering are discussed, mainly focusing on CL strategies and policy, green supply chain management, planning methods, and advanced concepts and practices. Finally, the research gaps framework and agenda were reported. This study contributes to summarizing the research and development of city logistics on the whole, and can also serve as an explorative manual to support sustainable urban freight activities and innovative research.