Over the past decades, China has been undergoing rapid economic growth, which may have significantly influenced the dietary patterns and health status of the Chinese population. Our study aimed to assess the associations of potential macronutrient trajectory patterns with chronic diseases and all-cause mortality using the latent class trajectory model (LCTM) and the longitudinal data of the China Health and Nutrition Survey obtained between 1991 and 2015. A 24-hour diet recall was used to assess the dietary intake. The Poisson regression model was employed to investigate the correlations between trajectory patterns and chronic diseases and all-cause mortality. A total of 8115 participants were included in the final analysis. We explored four and three trajectory patterns for male and female populations, respectively. We found that a decreasing very high-carbohydrate trajectory together with a U-shape protein trajectory was associated with a higher risk of diabetes in the male population (odds ratio (OR): 2.23; 95% confidence interval (CI): 1.31–3.77). A similar pattern for moderate protein intake was also associated with the risk of diabetes in the female population (OR: 1.82; 95% CI: 1.18–2.79). In addition, we show that a decreasing low-carbohydrate trajectory and an increasing high-fat trajectory were associated with a lower risk of all-cause mortality (OR: 0.76; 95% CI: 0.60–0.96) and a higher risk of obesity (OR: 1.24; 95% CI: 1.05–1.47) in males. Our results shed light on some salient nutritional problems in China, particularly the dual challenges of undernutrition and overnutrition.