High variation in population spatial distribution (i.e. less homogeneous spatial distribution) undermines population stability and resilience to a changing environment. Empirical studies suggest that sized-selective fishing contributes to age truncation, which in turn elevates population spatial variability for multiple fish species. We hypothesize that age-specific habitat preference (ontogenetic niche shift in habitat) contributes to such pattern. That is, different age classes of a fish population have distinct habitat choices. Size-selective fishing results in more right-skewed demography, which in turn increases the overall spatial patchiness (i.e. spatial heterogeneity) of the population. We further hypothesize that such effect is more pronounced when the population has a stronger age-specific habitat preference. To test these hypotheses, we devise a spatially-explicit, age-structured, multi-generational individual-based fish population model. Individual fish has either strong or weak age-specific habitat preferences. Survival rates of older age classes decrease with increasing fishing intensities. Supporting our hypothesis, spatial variability (coefficient of variation) increases with reducing age diversity (Shannon index), indicating fishing-induced age truncation elevates spatial variability. Furthermore, the sensitivity of spatial variability to age diversity is higher for population with stronger age-specific habitat preference. The differences in the sensitivity decrease with increasing carrying capacity and patchiness of habitat configuration.