In this study, a comprehensive 2-D chromatography was constructed, consisting of normal phase LC (NPLC) with a CN column as the first dimension, and supercritical fluid chromatography (SFC), with a Merck Chromolith Flash C(18) column as the second dimension, which were connected by a 10-port, dual-position valve controlled automatically by a self-designed software. Such platform was applied into the analysis of the fruiting bodies of Ganoderma lucidum, a traditional Chinese medicine, and within 2 h analysis, the obtained peak capacity of the 2-D-NPLC-SFC system was about 350, obviously higher than that of each dimension. These results demonstrate that 2-D-NPLC-SFC is not only of good orthogonality, but also of high throughput for the analysis of complex samples.