Abstract: To explore the general law of dynamic accumulation of the effective components in Stevia rebaudiana Bertoni, the contents of steviol glycosides, chlorogenic acids and flavonoids were investigated during the growth period. The leaf samples of Stevia rebaudiana Bertoni cultivar Puxing 6 from July 24 to October 16, 2018 were used as the subjects of high performance liquid chromatography analysis. In order to study clarification methods through analyzing the clarification rate and retention rate of three steviol glycosides and six chlorogenic acids, water extract of Stevia rebaudiana Bertoni was clarified by using five kinds of flocculants such as chitosan hydrochloride, chitosan quaternary ammonium, polyaluminum chloride (white), polyaluminum chloride (yellow) and ferrous sulfate plus calcium hydroxide. The results indicated that biomass showed an increased trend, and the contents of steviol glycosides showed a small fluctuation. The accumulation of chlorogenic acids and flavonoids was closely related to the growth period, and the contents presented decreased-increased-stabilized-decreased trend. The contents of steviol glycosides, chlorogenic acids and flavonoids reached the highest value from September 18 to October 2, which were 168.74, 73.78 and 14.88 mg/g respectively. According to the production and effective components, the optimal harvest time of Stevia rebaudiana Bertoni in Bazhou district of Xinjiang province should be from mid-September to early October. Different flocculants presented different clarification effects on water extract, and flocculating treatment of chitosan hydrochloride showed the highest retention rate of nine indicative components. The optimum condition obtained for chitosan hydrochloride were the dosage of 0.45 g/L and 45 ℃ temperature, and a clarification rate reached 89.39%. Chitosan hydrochloride could be used as a suitable flocculant for separation and purification of steviol glycosides and chlorogenic acids in water extract of Stevia rebaudiana Bertoni.