Objectives The prevalence of obesity was increasing globally, with nearly half a billion of the world’s population now considered to be overweight or obese. The immature poken (Citrus reticulata) was a good source of flavonoids and phenolic acids, which may exert an anti-obesity effect. However, the current efficacy in clinical trials was still unclear. Thus, the object of this study was to explore whether immature poken had an anti-obesity effect in the clinical trial. Methods In this study, we identified nine major compounds from immature poken extract (IPE), and most compounds significantly decreased the lipid accumulation in adipocytes. In addition, 20 subjects with body mass index (BMI) ≥ 24 or body fat > 30 were recruited and randomly allocated to placebo and experimental (IPE) groups for 6 week intervention and 2 week follow-up. Results In comparison with the baseline results (week 0), the body weight, body fat, and waist circumference at week 6 in the IPE group were significantly decreased by 1.49 kg, 0.33%, 2.1 cm. Moreover, in blood biochemical analysis, total cholesterol (TC), triglyceride (TG), fasting blood sugar (FBS), and insulin levels at week 6 in IPE group were also decreased by 3.6, 4.6, 2.1 (mg/dL), and 2.9 (μU/mL), respectively. Conclusions The finding showed that immature poken had important roles in fat metabolism by suppressing adipogenesis, and immature poken may provide new weight loss strategies for obese people.