Background: Lifestyles generally change across the life course yet no prospective study has examined direct associations between healthy lifestyle trajectories and subsequent cardiovascular disease (CVD) or all-cause mortality risk. Methods: Healthy lifestyle score trajectories during 2006–2007, 2008–2009, and 2010–2011 were collated through latent mixture modeling. An age-scale based Cox proportional hazard regression model was implemented to calculate hazard ratios (HR) with corresponding 95% confidence intervals (CI) for developing CVD or all-cause mortality across healthy lifestyle trajectories. Results: 52,248 participants were included with four distinct trajectories identified according to healthy lifestyle scores over 6 years i.e., low-stable (n = 11,248), high-decreasing (n = 7,374), low-increasing (n = 7,828), and high-stable (n = 25,799). Compared with the low-stable trajectory, the high-stable trajectory negatively correlated with lower subsequent risk of developing CVD (HR, 0.73; 95% CI, 0.65–0.81), especially stroke (HR, 0.70; 95% CI, 0.62–0.79), and all-cause mortality (HR, 0.89; 95% CI, 0.80–0.99) under a multivariable-adjusted model. A protective effect for CVD events was observed only in men and in those without diabetes, while a reduced risk of all-cause mortality was observed only in those older than 60 years, though interactions were not statistically significant. Marginally significant interactions were observed between the changing body mass index (BMI) group, healthy lifestyle score trajectories and stratified analysis. This highlighted an inverse correlation between the high-stable trajectory and CVD in BMI decreased and stable participants as well as all-cause mortality in the stable BMI group. The low-increasing trajectory also had reduced risk of CVD only when BMI decreased and in all-cause mortality only when BMI was stable. Conclusions: Maintaining a healthy lifestyle over 6 years corresponds with a 27% lower risk of CVD and an 11% lower risk in all-cause mortality, compared with those engaging in a consistently unhealthy lifestyle. The benefit of improving lifestyle could be gained only after BMI change is considered further. This study provides further evidence from China around maintaining/improving healthy lifestyles to prevent CVD and early death.