Background: Nitraria sibirica fruit is a kind of folk medicine widely used in Northwest China. It contains diverse kinds of bioactive constituents such as flavonoids, alkaloids, and phenols. Objectives: The research was performed to develop an efficient separation method for the bioactive constituents of N. sibirica fruit and evaluate the isolated compounds bioactivities. Materials and Methods: An optimized method of high-speed counter-current chromatography (HSCCC) combined with preparative high-performance liquid chromatography (HPLC) was established and applied to prepare the bioactive compounds from the ethyl acetate extract of N. sibirica fruit. The antioxidant and anticomplement activities of the isolated fractions and compounds were evaluated in vitro. Results: Ethyl acetate extract was the predominant antioxidant and anticomplement fraction of N. sibirica fruit, which yielded 18 compounds including six phenols, three flavonoids, and five alkaloids. Seven compounds (2, 4, 5, 9, 10, 12, and 17) were first isolated from genus Nitraria. Furthermore, under the optimized chromatography conditions, one anticomplement alkaloid (1) could be achieved directly by one-step HSCCC with high purity (92.34%), the other seventeen compounds were further purified with preparative HPLC. Ten compounds (3, 6, 7, 8, 9, 10, 11, 12, 13, and 14) exhibited significant antioxidant activities. Five compounds (1, 2, 7, 10, and 16) showed anticomplement activities and targeted different components in the complement system. Conclusion: The study provided an efficient method to prepare antioxidant and anticomplement compounds and the activities of the compounds were deeply investigated.