This study evaluates the performance of 6 global climate models (GCMs) from the Coupled Model Intercomparison Project Phase 6 (CMIP6) for simulating temperature, precipitation, wind speed, and relative humidity over 29 cities in Indonesia. Modern-Era Retrospective Analysis for Research Applications (MERRA-2) was considered as reference data to assess the city-wise performance of surface air temperature, precipitation, wind speed, and relative humidity simulated by the CMIP6 GCMs during 1980–2014. Six statistical measures were computed in this process (mean annual, seasonal amplitude, mean annual bias, root mean square error, correlation coefficient, and standard deviation). For 29 cities, the mean annual values of surface air temperature, precipitation, wind speed, and relative humidity obtained from the GCMs range between 290 to 302 K, 100 cm to 450 cm, 1 to 6 m/s, and 70 to 94%, respectively. The correlation coefficient between the GCMs and the surface air temperature (precipitation) reanalysis dataset ranges from 0.3 to 0.85 (−0.14 to 0.77). The correlation coefficient for wind speed (relative humidity) varies from 0.2 to 0.6 and is positive in some cases (0.2 to 0.8). Subsequently, the relative error that combines the statistical measurement results was calculated for each city and meteorological variable. Results show that for surface air temperature and precipitation, the performance of TaiESM was outstanding over the 10 or more cities. In contrast, for wind speed and relative humidity, NOR-MM and MPI-HR were the best over 7 and 19 cities, respectively. For all the meteorological variables, the performance of AWI was found to be worst over all the cities. The outcomes of this study are essential for climate-resilience planning and GCM selection while performing downscaling experiments. It will also be useful for producing updated national climate change projections for each city in Indonesia and providing new insights into the climate system.