Bitter melon (Citrullus colocynthis) Plant is of valuable medicinal plants that is adaptive with dunes of desert areas, that recommended as a treatment several diseases such as inflammation, arthritis and diabetes. In present research, different parts of this plant (stems, leaves, fruit and seeds), in two growth stage (flowering and seeding) ,from the two habitats in Sistan and Baluchestan Province in a completely randomized design with four replications were collected and, total flavonoid and antioxidant function of the plant were studied. Phenol content and total flavonoid of the methanol extracts were determined using spectrophotometry and antioxidant activity was determined using free radicals trap method. Statistical analysis was performed using version 18 of SPSS software and Factorial analysis of variance and mean comparisons were done by Duncan method. Results indicate that habitat, phonological stage and organ of plant have significant effect on antioxidant activity, Phenol content and total flavonoid of this plant, separately (p<0.01). Results revealed that interaction between habitat × plant's organ and habitat × phonological stages has significant effect on all phenolic and antioxidant compounds (p<0.05). According to the results, the highest antioxidant activity (44.77%) was observed in bitter melon's leaf extract of Saravan habitat.  The highest total phenol contentm (15.8 mg/g dray matter) was observed in stem extract of Zabol habitat, either. Moreover, the highest amount of flavonoid (12.73 mg/g dray matter) was observed in fruit extract of Zabol habitat. Results demonstrated that the extract of plant has the highest Phenolic and flavonoid compounds and antioxidant activity in flowering stage.