Objective To monitor the species composition and seasonality of calyptrate flies in four types of habitats in Yangpu district, Shanghai, China, and to provide a scientific strategy for fly control. Methods Cage traps were set up in the following four types of habitats: large-scale greenbelts (parks), greenbelts around restaurants, residential areas, and farm produce markets. Results A total of 1588 flies, belonging to 5 families, 25 genera, and 39 species, were captured from 2010 to 2013. The predominant strains were Muscina stabulans, Lucilia sericata, Aldrichina grahami, Anothomyia illocata, Chrysomya megacephala, and Muscina angustifrons. The seasonality showed peaks in June and September and the lowest population density in 2010. In the four types of habitats, the large-scale greenbelts showed the highest population diversity: 32 species, and the highest density was found in the farm produce markets with an average of 4.70 flies/cage·day. Conclusion The populations of calyptrate flies are abundant in habitats of Yangpu district, Shanghai. The predominant populations such as M. stabulans, L. sericata, and A. grahami should be the focus of fly control. Primary control measures should be taken in farm produce markets, and in June and September as the key time points for the prevention and control of fly-transmitted diseases.