Inhibiting the recombination of photo-generated charge carriers is crucial for improving the photocatalytic performance of materials. In this study, we ingeniously proposed a Ni, Zr co-doped graphite carbon nitride catalyst (CNNZ-x) with rich N vacancies (Vs). The analysis of the system shows that Ni, Zr co-doping and N Vs provide multiple channels for electron transfer, greatly promoting the efficient separation of photogenerated charges, promoting the generation of active species, and accelerating the degradation of TC. As a result, the optimized CNNZ1.2 almost completely removes TC within 30 min under visible light (λ ≥ 420 nm), with a corresponding first-order rate constant (k) of 0.2097 min−1, which is 9.71 times higher than pure CN (k = 0.0216 min−1). This TC removal performance is significantly higher than other CN-based photocatalysts reported in the literature. Furthermore, the CNNZ1.2 exhibits good cycling stability and adaptability under real-water conditions. The intermediates and three removal pathways of TC were analyzed by LC-MS and Fukui function. The E. coli culture experiment showed that the TC solution treated with CNNZ1.2 photocatalysis is almost non-toxic and does not cause secondary pollution to the water environment. These findings provide new insights into the design of CN-based photocatalysts and their efficient purification of antibiotic pollutants.