Understanding the mechanisms underlying spatial variability of exploited fish is critical for sustainable management of fish stocks. Empirical studies suggest that size-selective fishing can elevate fish population spatial variability through age truncation, making the population less resilient to changing environment. However, the underlying mechanisms remain unclear. We hypothesize that age-specific habitat preference, together with carrying capacity and environmental landscape structure, determines the response of population spatial variability to age truncation. To test these hypotheses, we design an individual-based model of an age-structured fish population on a two-dimensional landscape under size-selective fishing. Individual fish reproduces and survives, and moves between habitats according to age-specific and density-dependent habitat selection. The results show that population spatial variability elevates with increasing age truncation, and the response is stronger for the population with stronger age-specific habitat preference. On a continuous landscape, reducing carrying capacity elevates relative importance of density-dependence in habitat selection, which weakens the response of spatial variability to age truncation for populations with strong age-specific habitat preference. On a fragmented landscape, for populations of both strong and weak age-specific habitat preferences, fish individuals are restricted at local optimal habitats, and reducing carrying capacity weakens the responses of spatial variability to age truncation.