Many children suffer from nutritional deficiencies that may negatively affect their academic performance. This cluster-randomized controlled trial aimed to test the effects of micronutrient-fortified milk in Chinese students. Participants received either micronutrient-fortified (n = 177) or unfortified (n = 183) milk for six months. Academic performance, motivation, and learning strategies were estimated by end-of-term tests and the Motivated Strategies for Learning Questionnaire. Blood samples were analyzed for micronutrients. In total, 296 students (82.2%) completed this study. Compared with the control group, students in the intervention group reported higher scores in several academic subjects (p < 0.05), including languages, mathematics, ethics, and physical performance at the end of follow-up. Students in the intervention group showed greater self-efficacy and use of cognitive strategies in learning, and reported less test anxiety (p < 0.001). Moreover, vitamin B2 deficiency (odds ratio (OR) = 0.18, 95% confidence interval (CI): 0.11~0.30) and iron deficiency (OR = 0.34, 95% CI: 0.14~0.81) were less likely in the students of the intervention group, whereas vitamin D, vitamin B12, and selenium deficiencies were not significantly different. “Cognitive strategy” had a partial mediating effect on the test scores of English (95% CI: 1.26~3.79) and Chinese (95% CI: 0.53~2.21). Our findings suggest that micronutrient-fortified milk may improve students’ academic performance, motivation, and learning strategies.