How to improve the issues of ion agglomeration and metal ion leaching, and how to prepare cobalt-based catalysts with high reactivity and stability, are highly desired yet challenging. In this paper, MoS2 modified Co-MOF derived nitrogen-doped carbon (Co/PCN/MoS2) microspheres rich in active sites were prepared using a simple carbonation-hydrothermal method, with g-C3N4, MoS2 and Co-MOF to overcome the aforementioned limitations. The flower-like nanostructure of MoS2 contributed to exposing more marginal active sites, allowing the high dispersion of Co-MOF within its structure. Meanwhile, Mo4+/Mo6+ and S species coexisted in MoS2, which promoted the valence cycle and electron transfer process, and improved the catalytic activity of the composite. The successful synthesis of Co/PCN/MoS2 was proved by XRD, SEM and FTIR characterizations. The electrochemical performance analysis showed that Co/PCN/MoS2 exhibited higher redox capacity than MoS2, and Co/PCN/MoS2/PMS system achieved the degradation rate of RhB as high as 97.19% within 30 min, which is higher than that of Co-MOF/g-C3N4/PMS (80.67%), Co-MOF/MoS2/PMS (78.08%), Co-MOF/PMS (77.00%), g-C3N4/PMS (53.68%) and MoS2/PMS (28.10%) systems. It had good anti-interference ability against coexisting substances, achieved good degradation performance in a wide pH range (pH 2.0–10.0), and possessed excellent stability and reusability with RhB degradation rate of 91.10% after 5 cycles. The quenching test confirmed that non free radical 1O2 is the main ROS for RhB degradation. This work is expected to provide a new idea and direction for the design and development of metal-doped heterogeneous catalysts with high activity and stability.