High-throughput detection and screening of biological ingredients in a single bulk sample containing a wide range of taxa still have considerable problems. Recently, a new approach named “shotgun metabarcoding” combining shotgun sequencing and multiple barcodes has been proposed. Here, Shenling Baizhu San (SLBZS), a traditional patent medicine composed of ten plant and fungus ingredients was used to test its species detection capability. Mock and pharmaceutical samples of SLBZS were collected, and a total of 39.52 Gb of raw data were obtained via PCR-free shotgun sequencing. All ingredients made for mock samples can be successfully re-detected except Coix lacryma-jobi was failed to be detected in the second mock sample, and the positive control, the roots of Panax quinquefolius, can be re-detected in the second mock sample. For pharmaceutical samples, not only labeled ingredients but also adulterants, e.g. P. quinquefolius, were detected in a sample. The presence of P. quinquefolius was verified using the SNP detection method with a pair of Panax specific primers. In addition, 18 genera of fungal species were detected in both mock and pharmaceutical samples, however, the total number of fungal reads was relatively small. As a result, this study confirmed that shotgun metabarcoding could authenticate all the biological ingredients of SLBZS, has the potential to enable genomic analyses ideally of all species a single bulk sample.