Single atom catalysts (SACs) have been growing as an emerging "hot" topic in environmental remediation. Their performance can be rationally optimized via modulating spatial coordination configuration and the porous structure of SACs, which is still challenging. Herein, a novel Si, N co-coordinated cobalt SAC (p-CoSi 1 N 3 @D) with 3D free standing architecture is tailored via employing natural mineral (diatomite) as a Si source and porous template. Theoretical calculations and experimental analysis reveal that the substitution of N by Si dramatically accelerates the interaction and electron transfer between peroxymonosulfate and the Co single atom center. Moreover, p-CoSi 1 N 3 @D inherits the hierarchically porous architecture of diatomite, providing more accessible cobalt sites and open diffusion channels for peroxymonosulfate and contaminants in water treatment applications. Thanks to optimal coordination structure and porous architecture, p-CoSi 1 N 3 @D can serve as a highly active catalyst for peroxymonosulfate activation, with a turnover frequency of 299.8 min −1 for bisphenol A degradation, surpassing those of catalysts with transition metal SACs or oxides in the disclosed literature. This work provides a novel strategy for the development of SACs for wastewater reclamation, and deepens the understanding of the significant role of templates in spatial coordination configuration of SACs.