As a gel forming material, ginkgo seed protein isolate (GSPI) was used. Following the addition of γ-aminobutyric acid (GABA) and L-citrulline (L-Cit) to the GSPI solutions and homogenization, the pH of sols was adjusted to pH 5.0, 6.0, and 7.0, respectively. Heat-induced gels were prepared from these pre-treated samples. Physiochemical properties, mechanical mechanics, protein electrophoresis, SEM, and FTIR were used to determine the physiochemical characteristics, gelation, and microstructure of the mixture of GSPI/GABA and GSPI/L-Cit. A hypothesis was proposed to investigate how GABA, L-Cit, and pH influence gelation and potential mechanisms. The results have shown that GABA/L-Cit have no influential effects on protein solubility, but they have the ability to reduce their hydrophobicity; GABA promoted protein aggregation and lowered their ζ-potentials, whereas L-Cit assisted protein dissociation but also increased ζ-potential of the sols at pH 7.0. Moreover, the two amino acids facilitated the folding of hydrophobic groups inside the protein molecule. Additionally, the two amino acids, especially L-Cit, significantly enhanced protein gelation, but significantly decreased it when pH was 6.0. Variations in these changes can be attributed to a pH-dependent manner.