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Objective To analyze the relationship between dietary intake of n-3 polyunsaturated fatty acids (n-3 PUFA) and the incidence of type 2 diabetes mellitus (T2DM) among residents in selected districts of Chongqing, and to provide recommendations for the prevention of T2DM. Methods Using cross-sectional survey data collected in Chongqing as part of the 2021 China National Nutrition and Health Survey (CNNHS), and in combination with energy and nutrient intake calculated from the Chinese Food Composition Tables, single-factor and multi-factor Logistic regression models were employed to investigate the association between n-3 PUFA intake and the incidence of T2DM. Results This study included a total of 1 511 participants, of which 280 were diagnosed with T2DM, accounting for 18.80% of the total. When compared to participants in the lowest quartile of animal-derived n-3 PUFA intake, those in the highest quartile had a significantly lower risk of developing T2DM (OR = 0.61, 95% CI: 0.42-0.88). The results from adjusted Model 1 were consistent with those of Model 2 (Model 1: OR = 0.64, 95% CI : 0.44-0.94; Model 2: OR = 0.66, 95% CI: 0.44-0.98). Notably, in Model, the risk of developing T2DM was even lower in the Q4 group of plant-derived n-3 PUFA compared to Q1 (OR = 0.48, 95% CI: 0.24-0.98). Conclusion The dietary intake of animal-derived n-3 PUFA and plant-derived n-3 PUFA is negatively correlated with the incidence of T2DM. The association between animal-derived n-3 PUFA and T2DM weakens after adjusting for confounding factors, with the highest quartile of plant-derived n-3 PUFA showing the strongest protective effect against T2DM. [ABSTRACT FROM AUTHOR]