Odor problems are challenging issues in water treatment. Advanced oxidation has a significant degradation effect on these odors; however, some issues, such as oxidant residues and disinfection byproducts, exist in the use of advanced oxidation in actual water treatment. Because of the above issues, a combined advanced oxidation process has emerged—the UV/H2O2 -biological activated carbon (BAC) process can play a strong oxidizing role in advanced oxidation and uses the physical adsorption and biological effects of activated carbon. However, there have been few studies on the odor degradation mechanism and characteristics of activated carbon biofilms in actual water treatment. This paper systematically studied the organic and odor substances removal effects and mechanism of a pilot combined UV/H2O2-BAC process. The results showed that UV/H2O2-BAC technology had a good removal effect on odor substances under long-term stable operation. The concentrations of geosmin (GSM) and 2-methylisoborneol (2-MIB) after systemic treatment were below 5 ng/L. The removal rates of DOC, UV254 and H2O2 by the combined process were 53.60%, 73.08% and 60.20%, respectively. The results of full-scan determination of GSM and 2-MIB degradation by gas chromatography–mass spectrometry (GC–MS) were consistent with those of front-track analysis. The diversity, richness and evenness of microorganisms in the lower activated carbon layer were higher than those in the middle and upper activated carbon layers. The greater the difference in the carbon layer height was, the greater the difference in the biological community structure.