In this study, a rapid and highly sensitive ultra high performance liquid chromatography with triple quadrupole mass spectrometry method with the mobile phase of acetonitrile and 0.1% aqueous formic acid was established and successfully applied to comparatively analyze main active components after their compatibility. Besides, the effects of Scutellariae Radix, Coptidis Rhizoma and combined extracts on type 2 diabetic rats induced by high-fat diet along with low dose of streptozocin were investigated. Under the optimized chromatographic conditions, good separation of seven target components was achieved within 12 min. All calibration curves exhibited good linearity (R 2 ≥ 0.999). The relative standard deviation of precision, repeatability and stability varied from 0.69 to 2.23, 0.98 to 2.56, and 0.92 to 2.57%, respectively. The recovery ranged from 91.11 to 105.35%. The contents of seven active components were notably reduced after compatibility; however, the hypoglycemic effect of combined extracts was stronger than single drug by decreasing the activities of fructose-1,6-bisphosphatase, glucose 6-phosphatase, phosphoenolpyruvate carboxykinase and increasing the activities of glucokinase, phosphofructokinase, pyruvate kinase. Accordingly, the established analytical method was accurate and sensitive enough for quantitative evaluation of seven investigated compounds. Moreover, the combined extract had definite effects on type 2 diabetes through multiple components against multiple targets.