Heterogeneous Fenton catalysis offers a promising alternative to traditional Fenton oxidation for water treatment as its wider operating pH range and high cyclic performance. However, designing catalysts that can activate H2O2 both actively and selectively to mineralize refractory pollutants remains challenging. Here, a state‐of‐the‐art design principle of constructing spatially separated Fe‐M (M denotes an oxophilic first‐row transition metal) dual single‐atom sites is developed for Fenton‐like catalysis. This strategy enables accelerated redox cycles between the dual metal centers, leading to precise manipulation of Fe···O‐O···M intermediate in H2O2 activation. This, in turn, aids the homolytic decomposition of H2O2 toward selective and efficient •OH generation. Taking Fe‐Cu pairs as an example, the constructed dual sites outperform the individual Fe or Cu sites, demonstrating a higher activation selectivity (94%) for •OH production. Further benefitting from the electronic communications between Fe (electron acceptor) and Cu (electron donor), the SA‐Fe‐Cu‐CN catalyst exhibited an effective H2O2 decomposition with 0.94 mm of •OH yielded within 50 min. Compared to the typical homogeneous system, the SA‐Fe‐Cu‐CN/H2O2 system has higher mineralization capacities toward refractory pollutants and greater pH tolerance. The work provides a new strategy for the design of robust catalysts by creating spatially separated dual single‐atom sites toward multi‐reactant systems.