Objectives: We aimed to compare the quality of sleep, tongue diagnosis, oral microbiology differences in insomnia of Liver qi stagnation (LQS) and Non-Liver qi stagnation (NLQS). Methods: 56 patients were classified as LQS or NLSQ type insomnia through the insomnia differentiation questionnaire. The depression scores between the groups were compared through beck depression inventory (BDI), and the sleep quality was compared through Pittsburgh sleep quality index (PSQI) and Insomnia Severity Index (ISI). We analyzed the sleep efficiency, total sleep time, total awake frequency, total and average awake time through actigraph. For the tongue diagnosis, the distribution of tongue coating in six areas were measured through Winkel tongue coating index (WTCI). Linear discriminant analysis was performed to observe the differences in composition of microbial strains between the groups. Results: The scores of BDI, ISI and PSQI were significantly higher in LQS group. The total sleep time in LQS group was significantly less than that of NLQS group. Among the areas of tongue, according to the WTCI, the amount of tongue coating in zones A and C was significantly small. In oral microbial analysis, there was no significant difference between the groups at the phylum level. At the genus level, Prevotella, Veillonella, and Streptococcus were predominant in LQS group, whereas Prevotella, Neisseria, and Streptococcus in NLQS group. Conclusions: It was meaningful that insomnia was more likely in LQS group than in NLQS group, and the composition of oral microorganisms was significantly different, which could lead to the diseases caused by stress.