The present study examines the impact of meteorological conditions on future surface ozone (O3) over Malaysia region under RCP8.5 and RCP4.5 scenarios. The weather research forecast–community multiscale air quality (WRF-CMAQ) modelling system has been applied for the baseline period (year 2010) and the future day period (years 2050 and 2100) during the winter and summer monsoons. The simulation of WRF agrees well with observation datasets in simulating the surface temperature. However, precipitation did not perform well. The future projection revealed that the surface temperature increased across the Malaysian region, while patterns of total precipitation were varied. The study also identified model deficiencies of WRF-CMAQ in simulating air quality in the Malaysian region. RCP simulations reproduced the observed and reanalysis dataset for O3 mixing ratio with moderate values in statistical analysis. Compared with the present scenario, a small decrease in the O3 concentration was found under RCP8.5 scenario, while a large decrease was found for the RCP4.5 scenario except for the winter monsoon. In 2100, O3 reduced by − 1.4% (− 15.2%) and 4.5% (− 25.8%) during winter (summer) monsoons under the RCP8.5 and RCP4.5 scenarios, respectively. Overall, the decrease in O3 was found to be affected by meteorological change, as well as changes in ozone oxidants such as hydroxyl radical (OH), nitrogen oxides (NOx) and acid nitric (HNO3). Further tightening control measures on anthropogenic emissions to reduce future surface ozone may be unnecessary, since the future ozone mixing ratio did not exceed the Malaysia standard. However, continuous monitoring is vital to ensure efficient air quality management in Malaysia.