Free‐standing chitosan membranes were prepared using genipin as crosslinker, using several molecular weights of polyethylene glycol (PEG) as a void‐forming agent. The membrane surface formation and chitosan polymer chain crosslinking were confirmed through SEM and FTIR, respectively. The water flux was remarkably increased with increasing molecular weight of PEG employed in preparation of composite chitosan membrane (J∝[PEG(MW)]0.85), it appeared over 6000 Da of PEG. During Chlorella vulgaris harvest using chitosan membranes, focus was made on algae‐fouling caused by the deposition of cells and extracellular organic matter, and it was found that membranes employing lower molecular weight of PEG (under 10000 Da) had been maintaining the high flux recovery after alternating filtration cycles, in addition to PEG20000 containing membrane. The chitosan membrane prepared with lower molecular weight of PEG exhibited better suppression of algae‐fouling properties. The Chlorella vulgaris harvesting results indicated that cell rejection rate reached above 98%.