N-doping is a widely used strategy for the synthesis of highly efficient carbon nanocatalysts, however, an in-depth understanding of the effect of nitrogen source on the intrinsic structure and catalytic performance is highly desired. Therefore, to kill two birds with one stone, a series of N-doped carbon nanomaterials were synthesized from the pyrolysis of biomass waste (dealkali lignin) and various nitrogen sources (including melamine, dicyandiamide, and urea). Even though N-doping nanocatalysts showed better catalytic activity than the HCNs (pyrolysis form only dealkali lignin) for sulfamethoxazole (SMX) degradation via peroxymonosulfate (PMS) activation, NCN-1 and NCN-2 presented contractive and small spherical structures when melamine and dicyandiamide with high nitrogen content were added, showing relatively low catalytic efficiency. NPCN derived from dealkali lignin and urea led to the formation of a porous cluster structure with abundant active species of graphitic C/N and C-OH, which showed the best catalytic performance for SMX degradation. Significantly, NPCN exhibited excellent universality, adaptability, and reusability. Moreover, the possible mechanism was proposed based on the quenching study, EPR analysis, electronic quenching experiment, DFT calculation, and HR-MS, confirming that e−, 1O2, •OH, SO4•−, and O2•− were the active species, of which 1O2 was the dominating one in NPCN/PMS system. In addition, the biotoxicity of SMX was evaluated by the ECOSAR analysis and germination tests of wheat seeds. This work provides how the nitrogen source would affect the microstructure-dependent catalytic activity of metal-free carbon nanocatalysts for water decontamination.