Objective To establish the methods for controlling quality of Yiqi Congming Pills, and to improve the quality standard for the pills. Methods Yiqi Congming Pills were sampled from the products of 3 mainpharmaceutical companies in China market, 2 batched from each company. Radix Puerariae, Radix Astragali, Fructus Viticis, Cortex Phellodendri Chinensis, Radix Codonopsis in Yiqi Congming Pills were observed under microscope for microscopic identification. Radix Astragali, Rhizoma Cimicifugae, Radix Paeoniae Alba, and Cortex Phellodendri Chinensis were identified by thin-layer chromatography (TLC) for qualitative differentiation. The contents of puerarin and paeoniflorin in Yiqi Congming Pills were determined by high performance liquid chromatography(HPLC). Results The microscopic characteristics of Radix Puerariae, Radix Astragali, Fructus Viticis, Cortex Phellodendri Chinensis, Radix Codonopsis in the pills were obvious and were easy for discrimination. The spots in thin-layer chromatography (TLC) chromatograms of Radix Astragali, Rhizoma Cimicifugae, Radix Paeoniae Alba, and Cortex Phellodendri Chinensis were clear without interference of negative reference. Puerarin had a good linearity in the range of 0.00112~3.50676μg, and the average recovery rate was 98.2%(sR=1.4%, N=9 ). Paeoniflorin had a good linearity in the range of 0.00333 ~ 3.328 μg, and the average recovery rate was 98.4%(sR = 1.8%, N = 9). Great differences existed in the contents of puerarin and paeoniflorin of Yiqi Congming Pills from the three pharmaceutical companies. Conclusion The established qualitative and quantitative methods are of accuracy, credibility and repeatability, and are effective for controling the quality of Yiqi Congming Pills.