For persulfate-based advanced oxidation process, the non-radical pathway is an important route due to the selective oxidation of pollutants and its strong tolerance to complex water bodies. However, the selective oxidation mechanism of organic pollutants needs further elaboration. Herein, we demonstrate a facile hydrothermal pretreatment and high-temperature carbonization route to synthesize the nitrogen-doped porous biochar (NHBC-1). Owing to the well-developed hierarchical porous structure, the created internal active defects, and tailored nitrogen dopants, the NHBC-1 catalyst exhibited excellent catalytic activity for peroxydisulfate (PDS) activation. The results show that pyridinic N facilitated the adsorption of PDS on NHBC-1 to form the highly active NHBC-PDS* complex. Meanwhile, graphitic N and the defective structures promoted the electron-transfer process, thus allowing the efficient catalytic performance of the NHBC/PDS system for phenol oxidation via an electron-transfer dominated pathway. In addition, the system exhibited versatile applicability for the remediation of various organic pollutants in different actual water matrices with wide pH adaptability and satisfactory mineralization efficiency. More importantly, the selective oxidation mechanism of organic contaminants was revealed. Specifically, only the pollutant with oxidation potential lower than that of the NHBC-PDS* complex (0.91 V) can be effectively eliminated. This study not only provides a facile route for the rational designing of a cost-affordable biochar catalyst for PDS activation, but also offers valuable insights into the understanding of selective oxidation of organic contaminants via an electron-transfer dominated pathway.