Water-related disasters in urban area, especially urban floods have become more frequent and severe. This leads to loss of life, infrastructure damage, business interruption as well as difficulties in conducting daily activities. Phnom Penh, the capital city of Cambodia, has frequently experienced significant rainfall-flood events during rainy season. Without proper prevention and mitigation and management of urban drainage system, Phnom Penh is expected to confront with the current and future challenge of water-related disaster. To address this urban flood issue, flood modeling could be used to assess flood severity and make a visual representation of the urban flood hazard as basic information for land-use planning and limiting development in flood-prone areas. This study, therefore, aims to simulate flood events in a downtown area with the complex storm drainage system in Phnom Penh using FLO-2D model. The model was successfully calibrated and validated with time series data of water level in 2018 and estimated flood depth based on photo visualization through social media in 2015. The values of NSE, RMSE, and R2 were 0.76, 0.13, and 0.91 respectively. After model calibration, the model was used to simulate the flood flow through the channels, and floodplain within the study area in terms of flooding depth for 2-, 5-, 10-, and 25-year return periods of rainfall. The flood duration was determined by overlaying three flooding maps considered based on hydrograph components: rising flood, peak flood, and receding flood map. The result was delineated into flood hazard map defined by five categories, ranging from very low to very high. The result of flood hazard assessment shows that the floodplain under very low hazard category is constantly the highest one among all categories. However, with higher return period the flooding area under very low hazard category decreases while other hazard categories increase, especially medium hazard category increases significantly. The areas were found to have highest level of hazard are areas around Olympic stadium, areas around Royal Palace (along the river side), and areas in Beoung Trabek district. Besides, the simulated results show that the drainage system improved by JICA is capable to deal with the flood problem from the rainfall of 2-year return period in the study area.