Changes in the characteristics, removal efficiency, and toxicity of pharmaceutical effluent organic matter (EfOM) after catalytic ozonation were investigated in this study. After a 90-min treatment with a catalytic ozonation process (COP) in the presence of MnO2 ceramsite, the total organic carbon (TOC), UV254, colority, protein, and humic acid removal rates were 13.24%, 60.83%, 85.42%, 29.36% and 74.19%, respectively. The polysaccharide content increased by 12.73 mg/L during the COP for reaction times between 0 and ~50 min and decreased by 6.97 mg/L between 50 and ~90 min. Furthermore, 64.44% of the total colority was detected in the hydrophobic organic matter (HOM) fraction, and after the COP, and 88.69% of the colority in the HOM was eliminated. Meanwhile, only 59.18% of the colority in the hydrophilic organic matter (HIM) fraction was removed. GC-MS analysis showed that 38 organic pollutant species were completely removed, 8 were partially removed, and 7 were generated. After 90 min of COP treatment, the pharmaceutical EfOM toxicity was effectively reduced based on the higher incubation and lower mortality rates.