This study examined associations between academic stress and overweight and obesity, and moderation effects of gender, grade, and types of college on such associations. Data on academic stress, negative learning events, weight, and height were self-reported by 27,343 college students in China in 2018. About 23% and 91% of students perceived high academic stress and suffered from at least one negative learning event during the past six months, respectively, especially for females, undergraduates, and students major in humanities and social science subject groups. Perceived academic stress was associated with increased risk of overweight and obesity among all students (OR = 1.05, 95%CI: 1.00–1.10), male (OR = 1.09, 95%CI: 1.03–1.15), undergraduate (OR = 1.06, 95%CI: 1.00–1.11), and students from subordinate universities (OR = 1.13, 95%CI: 1.01–1.26). Negative learning events were associated with increased risk of overweight and obesity among all students (OR = 1.05, 95%CI: 1.01–1.09), undergraduates (OR = 1.05, 95%CI: 1.01–1.09), and students from local universities (OR = 1.07, 95%CI: 1.00–1.14). Interventions are needed to reduce the high academic stress of college students, considering the modifying effects of gender, grade, and college type. Such interventions may further contribute to the prevention of overweight and obesity among college students.