Ginkgo seed was used as raw foodstuffs to exact their proteins. The resulting ginkgo seed protein isolate (GSPI) was then subjected to pH-shifting treatments followed extreme acid (pH 2.0, pH 3.0, pH 4.0) or extreme alkaline (pH 10.0, pH 11.0, pH 12.0) by holding 2 h and then the pH was recovered to neutral. The solubility and emulsifying properties of pH-shifted GSPI were investigated. Upon the aqueous solutions (containing 0.5 mol/L NaCl), the physical and chemical analysis, spectroscopy and electrophoresis techniques were employed to detect the physical and chemical properties of the ginkgo protein solution to characterize the hydration properties, molecular components and structural modifications of the ginkgo protein isolate, as well as the aggregation behavior and emulsifying properties of the protein molecules, and investigate the effect of extreme acid and alkaline pH-shifting on protein structure and functionality thereof. The result indicated that extreme acid and alkaline pH-shifting processes cause the rise of protein hydrophobicity, sulfhydryl group content and fluorescence intensity, promotes protein unfolding, rearrangement and disclose their hydrophobic groups to form a disulfide-mediated aggregation, led to markedly improved solubility (particularly, the solubility is up to 31.91% from 13.42% of the control) and approximately 2-fold emulsion activity but decreased emulsion stability.