Utilization of semiconductor photocatalyst materials to degrade pollutants for addressing environmental pollution problems has become a research focus in recent years. In this work, a 2D/2D S-scheme crystalline carbon nitride (CCN)/BiOIO3(BOI) van der Waals heterojunction was successfully constructed for effectively enhancing the degradation efficiency of antibiotic contaminant. The as-synthesized optimal CCN/BOI-3 sample exhibited the highest efficiency of 80% for the photo-degradation of tetracycline (TC, 20 mg/L) after 120 min visible light irradiation, which was significantly higher than that of pure CCN and BOI. The significant improvement in photocatalytic performance is mainly attributed to two aspects: (i) the 2D/2D van der Waals heterojunction can accelerate interface carriers’ separation and transfer and afford sufficient active sites; (ii) the S-scheme heterojunction elevated the redox capacity of CCN/BOI, thus providing a driving force for the degradation reaction. The degradation pathways of TC for the CCN/BOI composite were investigated in detail by liquid chromatography-mass spectrometry (LC-MS) analysis. This work provides a design idea for the development of efficient photocatalysts based on the 2D/2D S-scheme van der Waals heterojunctions.