This study aims to address the existing gaps in evidence regarding spatio-temporal modeling of COVID-19 spread, specifically focusing on the impact of different urban land uses in a geospatial information system framework. It employs an agent-based model at the individual level in Gorgan, northeast Iran, characterized by diverse spatial and demographic features. The interactions between human agents and their environment were considered by incorporating social activities based on different urban land uses. The proposed model was integrated with the susceptible–asymptomatic–symptomatic–on treatment–aggravated infection–recovered–dead epidemic model to better understand the disease transmission at the micro-level. The effect of various intervention scenarios, such as social distancing, complete and partial lockdowns, restriction of social gatherings, and vaccination was investigated. The model was evaluated in three modes of cases, deaths, and the spatial distribution of COVID-19. The results show that the disease was more concentrated in central areas with a high population density and dense urban land use. The proposed model predicted the distribution of disease cases and mortality for different age groups, achieving 72% and 71% accuracy, respectively. Additionally, the model was able to predict the spatial distribution of disease cases at the neighborhood level with 86% accuracy. Moreover, findings demonstrated that early implementation of control scenarios, such as social distancing and vaccination, can effectively reduce the transmission of COVID-19 spread and control the epidemic. In conclusion, the proposed model can serve as a valuable tool for health policymakers and urban planners. This spatio-temporal model not only advances our understanding of COVID-19 dynamics but also provides practical tools for addressing future pandemics and urban health challenges.