Oxytropis microphylla (Pall.) DC. is a traditional Tibetan medicine used as an external preparation for clearing heat and detoxification, healing sore muscles, astringent vein hemostasis, defecation, and treating plague, constipation, anthrax, and swollen and painful furuncles. It remains a challenge to comprehensively analyze and identify the chemical constituents of Oxytropis microphylla (Pall.) DC. In this study, a new analytical method using a combination of ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS) and effective data mining techniques was established to identify the chemical constituents of Oxytropis microphylla. A total of 127 compounds were identified in O. microphylla extract, including 92 flavonoids, 15 indole alkaloids, and 20 others. After the oral administration of the extract to rats, 22 metabolites were identified in the plasma. The primary in vivo metabolic reactions that occurred after the administration of O. microphylla extract were glucuronidation and sulfation. Therefore, we successfully devised a high-efficiency method to distinguish compounds and used it as a source of post-study to identify the active biological components of O. microphylla extract.