This study synthesized novel, green, and easily recoverable surface-modified economical catalysts via hydrothermal treatment (HT) successfully, utilizing biogas residue biochar (BRB), a food waste product from anaerobic fermentation, pyrolyzed at 500 °C for 50 min. Using autoclaves, a total of six solutions were prepared, each having 1 g fine-grinded BRB, surficial modified by adding glycerol (GL) (10 or 20 mL) and SDI water (70 or 60 mL), and heated in an oven at 240 °C, 180 °C, and 120 °C for 24 h. Afterward, the catalysts showed the potential for degradation of widely used emerging pollutants like ciprofloxacin. Taking advantage of catalytic surface modification, the catalytic ozonation degradation was more effective than that of a single ozonation. However, under similar conditions, catalyst amount 0.20 g, ozone dose 15 mg L−1, and ciprofloxacin 80 mg L−1, the performance of the 10 mL GL-180 °C catalyst was excellent. It showed a 92.45%–94.41% optimum removal rate in the 8–10 min interval. After five continuous cycles, the 10 mL GL-180 °C catalyst exhibited excellent stability and reusability. XPS, FT-IR, BET, XRD, and SEM before and after the reaction confirmed the successful synthesis and degradation mechanism. A possible degradation pathway was unrevealed based on a liquid chromatography-mass spectrometer (LC-MS) and scavenger test, proving the significant roles of superoxide radicals (O2•-), hydroxyl radicals (•OH), and singlet oxygen (1O2). Further, Electron paramagnetic resonance (EPR) analysis confirmed the presence of active oxygen species. Subsequently, 10 mL GL-180 °C showed promising degradation for the actual water environment, such as groundwater (73.55%) and river water (64.74%). This work provides a valuable economic strategy to convert biogas residue biochar into a low-cost catalyst for organic pollutant decomposition.