Adsorption of polar molecules, such as formaldehyde, ammonia, and water, is profoundly affected by both the pore structure and the functional groups (FGs) of an adsorbent. Investigating the effects of pore structures and FGs separately is important but intractable for experiments and the conventional modeling. Molecular simulation provides a powerful tool to probe the adsorption mechanism by extracting abundant microscopic details. In present study, we have conducted a Monte Carlo simulation of formaldehyde, ammonia, and water, aiming to offer new insights into the capture of polar indoor air pollutants by adsorption. Upon the adsorption isotherms of formaldehyde and ammonia in the carbon nanopores at sub-ppm level, the effects of pore size and the FGs were separately investigated using the isosteric heats at zero loading as a measure of guest–host interaction. Based on the analysis of the pairwise potential energies of formaldehyde, ammonia, and water as well as their cluster-mediated adsorption mechanisms, we proposed that water may act as strong anchors for capturing formaldehyde and ammonia, with the premise that water does not condense and block the pore. Further discussion on the development of effective water-resistant adsorbent for the polar indoor air pollutants was presented.