Hongmu, a Chinese customary noun representing 29 kinds of wood species such as some Pterocarpus species (abbreviated as spp. hereinafter), Dalbergia spp. and Diospyros spp., is popular among Chinese people due to the furniture made from it. The slow regeneration of hongmu resources led to a decline in production, making hongmu prices high and illegal businesses profit from it. Therefore, it is necessary to identify and distinguish different varieties of hongmu for commercial trade. Herein, a cost-effective and rapid methodology was first developed via atmospheric pressure glow discharge mass spectrometry (APGD-MS) to classify three Dalbergia spp. and three Pterocarpus spp. Meanwhile, principal component analysis (PCA) was further applied to distinguish wood species and six kinds of hongmu extracts were able to be approximately separated into six units. Besides, hongmu could be clearly distinguished from their counterfeits, such as Guibourtia spp., using the method provided here. This method may provide a timely and necessary way for the determination of ingredients and identification of the authenticity of hongmu.