The urban model inter-comparison study (UMICS) was conducted in order to improve the performance of air quality models (AQMs) for simulating fine particulate matter (PM2.5) in the Greater Tokyo Area of Japan. UMICS consists of three phases: the first phase focusing on elemental carbon (UMICS1), the second phase focusing on sulfate, nitrate and ammonium (UMICS2), and the third phase focusing on organic aerosol (OA) (UMICS 3). In UMICS2/3, all the participating AQMs were the Community Multiscale Air Quality modeling system (CMAQ) with different configurations, and they similarly overestimated PM2.5 nitrate concentration and underestimated PM2.5 OA concentration. Various sensitivity analyses on CMAQ configurations, emissions and boundary concentrations, and meteorological fields were conducted in order to seek pathways for improvement of PM2.5 simulation. The sensitivity analyses revealed that PM2.5 nitrate concentration was highly sensitive to emissions of ammonia (NH3) and dry deposition of nitric acid (HNO3) and NH3, and PM2.5 OA concentration was highly sensitive to emissions of condensable organic compounds (COC). It was found that PM2.5 simulation was substantially improved by using modified monthly profile of NH3 emissions, larger dry deposition velocities of HNO3 and NH3, and additionally estimated COC emissions. Moreover, variability in PM2.5 simulation was estimated from the results of all the sensitivity analyses. The variabilities on CMAQ configurations, chemical inputs (emissions and boundary concentrations), and meteorological fields were 6.1-6.5, 9.7-10.9, and 10.3-12.3%, respectively.