<p>Pelagic fish are the most abundant species in upwelling regions, contributing 25% of total global fisheries production. Climate-driven changes in the marine environment play a crucial role in their population dynamics. Using Chilean jack mackerel (<i>Trachurus murphyi</i>) as an example, this study conducted simulations to quantify the impacts of environmental variations on the stock assessment. A habitat-based surplus production model was developed by integrating suitable habitat area into the model parameters carrying capacity (<i>K</i>) and intrinsic growth rate (<i>r</i>), with a suitable habitat area serving as the proxy for the environmental conditions for Chilean jack mackerel in the Southeast Pacific Ocean. The dynamics of Chilean jack mackerel stock and fisheries data were simulated, and four assessment models with different configurations were built to fit simulated data, with or without considering environmental effects. The results indicated that Joint K-r model, which integrated both parameters with the suitable habitat area index, outperformed the others by coming closest to the ‘true’ population dynamics. Ignoring habitat variations in the estimation model tended to overestimate biomass and underestimate harvest rate and reference points. Without observation and process error, the results were estimated with bias, while <i>F</i>_MSY is relatively sensitive. This research illustrates the importance to consider random errors and environmental influences on populations, and provides foundation guidelines for future stock assessment.</p>