Currently, adopted runoff analysis models focus on the characteristic factors of watersheds and neglect the analysis of the flow in conduits. Additionally, the usually employed XP-SWMM modeling package generally underestimates the flood area because it considers manholes as nodes and does not consider local head losses according to the shape and size of the nodes. Therefore, it is a necessity to consider the loss coefficient in surcharge manholes to improve inundation and runoff analysis methods. This study aims at improving the accuracy of discharge analysis before analyzing the storage and runoff reduction effects of storage facilities. Hydraulic experiments were conducted according to the changes in discharge and manhole shapes. We show that the flood area increases as the overflow discharge at manhole increases due to the application of the head loss coefficient. We demonstrate a concordance rate ≥95% between results and observed flood area when accurate input data (from the parameters of the target watershed) and the head loss coefficient (from hydraulic experiments) are applied. Therefore, we demonstrate that the result of our 2D inundation analysis, considering the head loss coefficient in surcharge manhole, can be used as basic data for accurately identifying urban flood risk areas.