In this study, Bacillus subtilis natto was encapsulated in alginate, either coated with or mixed with xanthan gum as a supplemental component. The encapsulated bacteria were then evaluated for their survival in simulated gastric fluid (SGF) and simulated intestinal fluid (SIF). The results showed that B. subtilis natto biomass had a thrombolytic ability compared to the control sample. The viability of encapsulated B. subtilis natto was improved in which alginate 2.5% (w/v) had a high encapsulation efficiency, and there was no difference between the samples with or without the xanthan gum supplement. In the SGF and SIF tests, the viability of B. subtilis in samples supplemented with xanthan gum was higher than in samples that contained only alginate. Additionally, there was no significant difference in viability between the samples that mixed xanthan gum with alginate and those that were coated with it. The results indicated that adding xanthan gum is necessary to increase alginate's protective effect on B. subtilis natto.