Rectification of surface chlorophyll (Chl) concentration by the atmospheric intraseasonal variability is detected in a numerical biophysical ocean model when it is forced by composite Madden-Julian Oscillation (MJO) events. In addition to the shoaled mixed layer depth (MLD) previously reported, it is found that increased mean Chl by MJO forcing mostly co-occurs with shoaled isothermal depth (ITD) / nutrient isopleths and reduced barrier layer thickness (BLT). Case studies reveal that MJO forcing increases MLD and ITD variations, which enhances vertical mixing and brings nutrients to the surface layer thereby increasing Chl concentration. The shoaled MLD and ITD in the seasonal / annual mean are due to asymmetric responses to MJO wind forcing; i.e., shoaling by weaker wind is more sensitive than deepening by stronger wind. Reduced mean BLT is because ITD shoaling is larger than MLD shoaling. As an exception, it is detected that both the mean Chl and BLT are increased by MJO forcing in the southern Bay of Bengal. Here, the ITD is climatologically deep in the active MJO season (boreal summer), and different phase between the MLD and ITD variations results in temporarily large BLT. However, this barrier layer does not effectively isolate the surface layer from the nutrient-rich deeper ocean. Lastly, observations support our findings in limited regions and seasons, though further investigation is necessary to confirm the effect of atmospheric intraseasonal variability on the mean surface Chl.