In this study, citrus pectin (CP) and soybean protein isolate (SPI) were used as raw materials to prepare a complex. The interaction mechanism and structural changes between SPI and CP were deeply studied by fluorescence spectroscopy and Fourier infrared spectroscopy. The results show that CP has a strong quenching effect on SPI's endogenous fluorescence, and with the addition of CP, the endogenous fluorescence intensity of SPI decreased from 13,565.2 to 6067.3. The CP quenching of SPI is static quenching, and the number of combined bits is 1.26. The results of three-dimensional fluorescence spectra showed that the addition of CP reduced the polarity of SPI amino acid residue microenvironment and changed the protein structure. Hydrophobic interaction exists between CP and SPI. The results of three-dimensional fluorescence spectra showed that the addition of CP reduced the polarity of the amino acid residue microenvironment of SPI and changed the protein structure. Fourier transform infrared spectroscopy shows that CP could change the secondary structure of SPI by decreasing the α-helix and β-sheet, increasing β-rotation and irregular curl, destroying the ordered structure of SPI and increasing the polarity of the amino acids exposed to the solution. The microstructure analysis shows that SPI-CP composite system has honeycomb structure and dense pores. From the perspective of reaction thermodynamics, it was found that the addition of CP could improve the thermal stability of SPI and increase the denaturation temperature of SPI from 119.73 to 132.97°C. This study can provide a theoretical basis for the preparation of protein-pectin complexes and provides reference for their application in food grade gels and Pickering emulsions.