In recent years, advanced oxidation technologies employ peroxynitrite activation have exhibited exceptional effectiveness in eliminating various emerging contaminants. In this study, different calcination temperatures were used to derive Co3O4 nanospheres with varying surface morphologies. This method effectively addresses the issue of high cost associated with high-performance catalyst synthesis or poor catalytic performance of low-cost catalysts. The active species like O2•−, •OH, SO4•−, 1O2 played significant role in TC degradation and 1O2 was the dominant reactive oxygen species (ROS). The study also proposed possible degradation pathways based on the 15 intermediates identified through HPLC-MS. Furthermore, the developmental toxicity of the identified intermediates was evaluated using a quantitative conformational relationship prediction method. This paper delves into the reaction mechanism of Co3O4 nanospheres in the activation of PMS and examines the impact of surface morphology on their catalytic performance, providing a new approach to developing a persulfate catalyst that is cost-effective and has high catalytic performance, with a simple synthesis step.