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This study systematically investigated the impact of covalent binding of tannic acid (TA) to different proteins on protein structure and the stability of a nanoemulsion of Perilla essential oil (PEO). Additionally, the antimicrobial activity of the nanoemulsion was assessed. The interactions between TA and various proteins were explored using fluorescence spectroscopy and Fourier transform infrared (FTIR) spectroscopy, revealing that TA exhibited the most binding sites (n = 1.65) to whey protein isolate (WPI), forming a stable protein-TA complex. The emulsion prepared using TA had high stability. One-factor-at-a-time experiments showed that the emulsion prepared under the conditions of 675 W ultrasonic power and an oil-to-water ratio of 1:9 had the smallest droplet size of (292.3 ± 1.96) nm, a relatively high absolute zeta potential value of (–62.5 ± 0.29) mV, and the highest PEO encapsulation efficiency of (74.51 ± 0.35)%. The interaction between WPI-TA complex and PEO could stabilize the structure of the emulsion, and the emulsion maintained high stability at 4 ℃ for 28 days. Furthermore, emulsion encapsulation significantly reduced the loss of PEO, with the loss of PEO in the emulsion being only one-third of that of the pure essential oil under the same conditions. This study provides new ideas for future research on the synthesis of protein-polyphenol complexes and the encapsulation of volatile substances, laying a foundation for expanding the application of nanoemulsion in the food industry.