Both indoor unclean fuel use and CVD associates with cognitive function. Indoor fuel has transitioned from the use of unclean fuel to clean fuel in recent years in China. The aim of this study was to evaluate the association between adult cognitive function and such a transition and to investigate the potential role of CVD in this association. 7112 participants (26- to 98-years of age) with 12,676 observations living in twelve provinces of China from 1997 to 2015 were extracted based on having complete data. The associations, combined effects, and further mediation effects between indoor unclean fuel use and its transition, CVD, and cognitive function were tested using regression models, stratified analyses, the relative excess risk due to interaction (RERI), mediation analysis methods, and sensitivity analyses. Between 1997 and 2015, cooking fuel use coal and wood went down a lot in China, from a baseline of 26.9% to 6.1%, from 30.1% to 11.5%, respectively. Such a transition showed a positive association with delayed verbal recall (B = 0.288, p < 0.01), especially in rural area, subjects with age ≥ 65 years old, and women (all P < 0.05). The combined effect of the presence of hypertension during a baseline visit and such a transition on changes in delayed verbal recall was antagonistic (RERI = -0.529, p < 0.05). Moreover, the development of hypertension explained more than 50% of such a fuel transition-related decline of verbal memory. The transition of household energy to clean fuel was associated with a higher adult cognitive function. The presence or the development of CVD appeared to affect the association between indoor air pollution and cognitive function, which suggests a need to further optimize prevention of concurrent CVD and risk factor control in adults at higher risk for cognitive impairment and with indoor unclean cooking fuel, especially in potentially susceptible subgroups.