Background: School-based green space activities have been found to be beneficial to the physical activity level and lifestyle habits of adolescent students. However, their effects on green space use and satisfaction, mental health, and dietary behaviors required further investigation. This study aimed to investigate the effects of school-based hydroponic planting integrated with health promotion activities in improving green space use, competence and satisfaction, healthy lifestyle, mental health, and health-related quality of life (QoL) among early adolescent students in secondary schools.Methods: This study adopted a three-group comparison design (one control and two intervention groups). Secondary school students (N = 553) of grades 7–9 participated in either (1) hydroponic planting (two times per week for 8 months) integrated with health promotion activities; (2) only health promotion activities (one time per week for 6 weeks); or (3) control group. Outcomes assessed by questionnaire included green space use and satisfaction, life happiness, lifestyle, depressive symptoms, and health-related QoL.Results: After adjusting for sex and school grade, the scores in “green space distance and use” and “green space activity and competence” were significantly better in the intervention groups than in the control group. Hydroponic planting integrated with health promotion activities was also associated with better scores in dietary habits and resistance to substance use. Intervention groups had a higher score in “Green space sense and satisfaction” and life happiness when compared with the control group.Conclusions: Our study shows that the school-based hydroponic planting integrated with health promotion activities were feasible and, to a certain extent, useful to improve green space use and competence, dietary habits, and resistance to substance use among early adolescent students in secondary schools in urban areas. Future studies should address the limitations identified, for example, designing a randomized controlled trial that could fit school schedules to generate new evidence for physical and mental health in adolescent communities.