Inadequate intake of fruits and vegetables (FV) and moderate-to-vigorous physical activity (MVPA) in children has become a global public health problem. Therefore, school-based gardening and cooking (SGC) and sports participation (SP) interventions may be effective in improving children’s FV intake and MVPA. The aim of this study is to develop and evaluate the effectiveness of SGC and SP interventions on FV intake and MVPA among Chinese children. In this cluster randomized controlled trial study, 237 children in grades 4–5 from six public primary schools from Changsha, Hunan Province, China will be randomly assigned to: (1) a SGC and SP combined intervention group; (2) a SP intervention group; (3) a regular practice group. The intervention clusters will be implemented for a period of 6 months and follow up will be carried out after 12 months. The outcome will be collected using a combination of self-reported and objective measures. Primary outcomes will include children’s FV intake and duration of MVPA per day, and secondary outcomes will included frequency and attitudes of FV intake and SP, in addition to other measures. Finally, a process evaluation will be used to analyze the facilitators and barriers to intervention implementation. Trial Registration: (Registration Number: ChiCTR2200064141).