[Objective] This study aimed to compare and analyze the chemical compositions, the relative contents and the antibacterial activity of the essential oils extracted from the tissue culture seedlings, the aseptic seedlings and the common seedlings from seeds of Thymus vulgaris. [Method] The essential oil was extracted by steam distillation; the chemical compositions and their relative contents were analyzed by gas chromatography-mass spectrometry (GC/MS) and peak area normalization method; and the antimicrobial activity was tested by filter paper method. [Result] A total of 54 compositions were identified from these three samples, they had similar main compositions: thymol, m-Cymene, terpinene and so on, and these compositions were slightly different in contents. In addition, the essential oils from these three samples exhibited obvious antibacterial effect against Escherichia coli and Staphylococcus aureus, in which the antibacterial activity against S. aureus was stronger than against E. coli. [Conclusion] It is possible to produce essential oil by tissue culture technology; the main compositions and antibacterial activity of the oils remained almost the same.