The characteristics of dissolved organic matter (DOM) that formed during the aerobic and anaerobic incubation of drinking water treatment sludge stored at different temperatures (5 °C, 20 °C, 40 °C) for long periods (7, 14, and 21 days) were investigated. Anaerobic incubation at high temperatures with prolonged storage was found to result in higher organic content than aerobic incubation (3.6–6.8 times at 40 °C). The high temperatures caused changes in the DOM fractions, with humic-like substances mainly formed in aerobic incubation and protein-like substances in anaerobic incubation. Results showed that the fluorescence intensity of humic-like and protein-like substances increased by 45% and 22%, respectively, at the end of the anaerobic incubation period. The UV-absorbing DOM constituents in aerobic incubation had lower molecular weights and were more heterogeneous than those in anaerobic incubation.