Semen Platycladi is a widely used natural product in Chinese medicine with pharmacological effects such as anti-arteriosclerosis, sleep improvement, antioxidant and anti-inflammatory. The quality of Semen Platycladi is fundamentally important for its therapeutic use. However, the tedious sample pretreatment required by the currently available methods poses great challenge to the high throughput analysis and evaluation of the quality of Semen Platycladi. Here we establish a high-throughput analysis platform for evaluating the quality of various Semen Platycladi samples using Internal Extractive Electrospray Ionization Mass Spectrometry (iEESI-MS). The fatty acids including linoleic acid, linolenic acid, arachidonic acid, stearic acid and palmitic acid, known as one of the major ingredients in Semen Platycladi, were directly quantified in the range of 0.001-100.00 μg mg