An antimicrobial capsule releasing thyme oil was developed using modified halloysite nanotubes (HNTs). In order to increase the pore volume, HNTs were treated with 5.0 mol/L NaOH solution, which resulted in the encapsulation of more thyme oil molecules inside the HNTs. The morphology of the raw HNTs and NaOH-treated HNTs (N-HNTs) was characterized using transmission electron microscopy and nitrogen adsorption-desorption analysis. The loading capacity increased from 180.7 ± 12.7 to 256.4 ± 16.7 mg thyme oil/g HNT after the NaOH treatment. The aerial release characteristics of thyme oil from both the HNT capsules were investigated in a closed-package atmosphere system at 4, 25, and 40 °C. The antimicrobial activity of the capsule against Escherichia coli O157:H7 was determined using the vapor phase assay. Moreover, the antimicrobial effects of the capsule against E. coli O157:H7, total mesophilic aerobic bacteria (MAB), and molds and yeasts (MY) on the surfaces of cherry tomatoes were investigated at 4 and 25 °C for 5 d. When the cherry tomatoes were exposed to the thyme oil-loaded N-HNT capsule, the number of E. coli O157:H7, MAB, and MY significantly reduced during storage.