Habitat loss is a critical driver of biodiversity decline; yet, its impact on species coexistence remains complex. We systematically investigated the effects of symmetric and asymmetric habitat loss on both well-mixed and structured populations using the rock–paper–scissors game model. In well-mixed populations, theoretical analysis identified various equilibrium states whose stability is governed by the interplay between habitat-loss intensity, predation, the rates of species mortality, and reproduction. Monte Carlo simulations of structured populations demonstrated that increasing habitat loss significantly disrupts the coexistence of the three species, leading to spatial fragmentation. Notably, asymmetric habitat loss exhibited unique stabilizing effects, promoting the coexistence of two species or the persistence of a single species. Our findings underscore the intricate and nonlinear interactions between habitat loss and species dynamics, highlighting the necessity of incorporating environmental degradation into biodiversity conservation strategies.