Abstract: A method of atmospheric pressure chemical ionization mass spectrometry (APCI-MS) was established for analyzing Compound Indigowoad Root Granule extract, and the main peaks in the fingerprints were confirmed by high performance liquid chromatography coupled to mass spectrometry hyphenated (LC-APCI-MSⁿ). The fingerprint analysis was based on the atmospheric pressure chemical ionization ion source (APCI) with the positive mode. The separation was performed on a Kromasil C18 column (4.6 mm×25.0 mm×5 μm) under 25 ℃ with linear gradient elution of methanol (containing 0.15% acetic acid) water as mobile phase at a flow rate of 0.8 mL/min. The detector is full wavelength ultraviolet detector (DAD) with the detection wavelength of 254 nm. Mass spectrometry analysis was required for atmospheric pressure chemical ionization ion source (APCI) with both positive and negative ions detection modes. Mass spectrometry fingerprint identified 10 common peaks from 10 batches of different sources of Compound Indigowoad Root Granule extracts and the results showed that the similarities of each extract was covered over 97%. A total of 12 chemical compounds, including indoles, quinazolinones organic acids and porphyrins were identified using LC-APCI-MSⁿ, and 5 common fingerprint peaks were identified. Pharmacodynamical studies have revealed that extracts of Compound Indigowoad Root Granule own certain anti-viral activities. Hense, owing to its high precision, stability and reproducibility, the fingerprint method in Compound Indigowoad Root Granule is important and indispensable in the foundation of quality control standards as well as the further research in the relationships of material basis and spectrum effect.