With the spatial structure of urban agglomerations, well-developed transportation networks and close economic ties can increase the risk of intercity transmission of infectious diseases. To reveal the epidemic transmission mechanism in urban agglomerations and to explore the effectiveness of traffic control measures, this study proposes an Urban-Agglomeration-based Epidemic and Mobility Model (UAEMM) based on the reality of urban transportation networks and population mobility factors. Since the model considers the urban population inflow, along with the active intracity population, it can be used to estimate the composition of urban cases. The model was applied to the Chang-Zhu-Tan urban agglomeration, and the results show that the model can better simulate the transmission process of the urban agglomeration for a certain scale of epidemic. The number of cases within the urban agglomeration is higher than the number of cases imported into the urban agglomeration from external cities. The composition of cases in the core cities of the urban agglomeration changes with the adjustment of prevention and control measures. In contrast, the number of cases imported into the secondary cities is consistently greater than the number of cases transmitted within the cities. A traffic control measures discount factor is introduced to simulate the development of the epidemic in the urban agglomeration under the traffic control measures of the first-level response to major public health emergency, traffic blockades in infected areas, and public transportation shutdowns. If none of those traffic control measures had been taken after the outbreak of COVID-19, the number of cases in the urban agglomeration would theoretically have increased to 3879, which is 11.61 times the actual number of cases that occurred. If only one traffic control measure had been used alone, each of the three measures would have reduced the number of cases in the urban agglomeration to 30.19 %-57.44 % of the theoretical values of infection cases, with the best blocking effect coming from the first-level response to major public health emergency. Traffic control measures have a significant effect in interrupting the spread of COVID-19 in urban agglomerations. The methodology and main findings presented in this paper are of general interest and can also be used in studies in other countries for similar purposes to help understand the spread of COVID-19 in urban agglomerations.