The aim of the present study was to prepare a new antimicrobial Pickering emulsion of which the star anise essential oil was added to the oil phase, and to investigate the effect of stabilization by bio‐based active nanoparticles consisting of zein and pectin loaded with thymol. First, the thymol‐loaded zein/pectin composite nanoparticles (ZTNPs) were fabricated as uniformly distributed spherical nanoparticles with an average diameter of 200 nm through antisolvent precipitation. Second, the effects of nanoparticles’ concentration, oil phase ratio, and storage time on the stability of emulsions were explored according to particle size potential, interfacial tension, rheology, and micromorphology. Finally, the antibacterial results showed that Pickering emulsion inhibited Escherichia coli and Staphylococcus aureus compared to the control group by nearly 7 log colony‐forming unit/g at 36 h, which was twice as much as the inhibition by thymol or star anise essential oils and ZTNPs.. Therefore, the proposed Pickering emulsion with star anise essential oil could be used as a green and safe plant‐derived antimicrobial agent in the food industry.