Risk assessment of the intra-city spatio-temporal spreading of COVID-19 is important for providing location-based precise intervention measures, especially when the epidemic occurred in the densely populated and high mobile public places. The individual-based simulation has been proven to be an effective method for the risk assessment. However, the acquisition of individual-level mobility data is limited. This study used publicly available datasets to approximate dynamic intra-city travel flows by a spatio-temporal gravity model. On this basis, an individual-based epidemic model integrating agent-based model with the susceptible-exposed-infectious-removed (SEIR) model was proposed and the intra-city spatio-temporal spreading process of COVID-19 in eleven public places in Guangzhou China were explored. The results indicated that the accuracy of dynamic intra-city travel flows estimated by available big data and gravity model is acceptable. The spatio-temporal simulation method well presented the process of COVID-19 epidemic. Four kinds of spatial-temporal transmission patterns were identified and the pattern was highly dependent on the urban spatial structure and location. It indicated that location-based precise intervention measures should be implemented according to different regions. The approach of this research can be used by policy-makers to make rapid and accurate risk assessments and to implement intervention measures ahead of epidemic outbreaks. •The spatio-temporal simulation method based on available big data and gravity model well presented the process of COVID-19.•Four kinds of transmission patterns were identified and they were highly dependent on the urban spatial structure and location.•Location-based precise intervention measures should be implemented according to different regions.•The approach can be used by policy-makers to make rapid and accurate risk assessment and to implement intervention ahead of epidemic outbreaks.