Algal organic matter (AOM) released from microalgae has high potential effects for water treatment. In response to the complex problem of algal-laden water treatment, this study investigated the characteristics of AOM of Microcystis aeruginosa under long-term exposure to pharmaceuticals and personal care products (PPCPs). The results indicated that algae under low carbamazepine (10 µg/L), and/or diclofenac at any concentration treatment promoted the release of total organic matter, whereas they were inhibited at high carbamazepine and low naproxen exposure. Macromolecular organics of AOM were inhibited when algae were subjected to long-term exposure to carbamazepine at any concentration (0.25–1000 µg/L), and the higher the carbamazepine concentration was, the more seriously macromolecular organics were inhibited. For naproxen and diclofenac treatment, macro- and medium-molecular-weight organics were promoted under high concentration treatment (>1 µg/L), yet they were inhibited under low concentration 10 µg/L). This research had significant effects on algal-laden water treatment containing various PPCPs concentrations as well as the risk assessment of PPCPs in water.