This study investigated the effects of ultrasound on the self-assembly behavior of pea protein (PP)-high methoxyl pectin (HMP) complexes at pH 2.0 through transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FTIR), and intrinsic fluorescence analysis. The emulsion stabilization mechanism of PP-HMP treated with ultrasound (PP-HMP-US) was also elucidated. The results indicated that ultrasound increased the emulsifying activity index (EAI) and emulsifying stability index (ESI) of PP-HMP. Moreover, PP-HMP-US-based emulsions formed small, dispersed oil drops, which were stable during storage. PP-HMP- and PP-HMP-US-based emulsions did not demonstrate any creaming. The TEM results revealed that ultrasound can regulate the self-assembly behavior of PP and HMP to form spherical particles with a core–shell structure. This structure possessed low turbidity, a small particle size, and high absolute zeta potential values. The FTIR and intrinsic fluorescence spectra demonstrated that ultrasound increased the α-helix and β-sheet contents and exposed the tryptophan groups to more hydrophilic environments. Ultrasound also promoted the PP-HMP self-assembly through electrostatic interaction and improved its oil–water interfacial behavior, as indicated by the EAI and ESI values of PP-HMP-US-based emulsions. The current results provide a reference for the development of an innovative emulsifier prepared by ultrasound-treated protein–pectin complexes at low pH.