This study confirmed the discrepancy of growth period and molecular weight (MW) of extracellular organic matter (EOM) on the photodegradation of carbamazepine (CBZ) and theophylline (TF). Comparing to high MW EOM (100 kDa), low MW components (<100 kDa) acted as stronger competitors to photons and free radicals, which restrained the photodegradation of CBZ and TF. 3EOM* played an important role in the degradation of CBZ and TF. Lignin was considered as a new precursor of 3EOM*, which was highly depended on the MW of EOM. The high MW 3EOM* was derived from the CHON compound, while the low MW 3EOM* was derived from the CHONS compound. The results demonstrated that the discrepancy of EOM properties in algae growth period might play a non-negligible influence in the migration and transformation of CECs in the true natural water system.