Observational studies report a correlation between height and intelligence, but causality and mechanisms remain unclear due to confounding and reverse causation. Using large-scale genome-wide association study (GWAS) summary data, we performed bidirectional two-sample Mendelian randomization (MR) analyses and two-step mediation analyses to examine the associations between height and intelligence (general and fluid), and potential mediation by neuroticism, body mass index (BMI), anxiety, and major depression. Genetically predicted height was positively associated with intelligence (general intelligence: β = 0.115, p = 1.2 × 10−19; fluid intelligence: β = 0.266, p = 5.7 × 10−22). Height was negatively associated with neuroticism (β = −0.032, p = 7.0 × 10−5) and BMI (β = −0.067, p = .002), which were in turn negatively associated intelligence. Mediation analyses showed significant indirect effect of neuroticism (6.09%, p = 2.6 × 10−4) and BMI (7.83%, p = 6.0 × 10−3). No mediation was found for anxiety or depression. Reverse MR also suggested positive associations of intelligence with height. This study provides genetic evidence for bidirectional association between height and intelligence, with neuroticism and BMI as potential mediators. These findings improve our understanding of the height-intelligence relationship and its underlying psychological and metabolic pathways.