In this work, we extracted proteins from white quinoa cultivated in the northeast of Qinghai-Tibet plateau using the method of alkaline solubilization and acid precipitation, aiming to decipher how extraction pH (7–11) influenced extractability, purity and recovery rate, composition, multi-length scale structure, and gelling properties of quinoa protein isolate (QPI). The results showed that protein extractability increased from 39 to 58% with the increment of pH from 7 to 11 whereas protein purity decreased from 89 to 82%. At pH 7–11, extraction suspensions and QPI showed the similar major bands in SDS-PAGE with more minor ones (e.g., protein fractions at > 55 or 25–37 kDa) in suspensions. Extraction pH had limited effect on the secondary structure of QPI. In contrast, the higher-order structures of QPI were significantly affected, e.g., (1) emission maximum wavelength of intrinsic fluorescence increased with extraction pH; (2) surface hydrophobicity and the absolute value of zeta-potential increased with increasing extraction pH from 7 to 9, and then markedly decreased; (3) the particle size decreased to the lowest value at pH 9 and then increased to the highest value at pH 11; and (4) denaturation temperature of QPI had a large decrease with increasing extraction pH from 7/8 to 9/10. Besides, heat-set QPI gels were formed by loosely-connected protein aggregates, which were strengthened with increasing extraction pH. This study would provide fundamental data for industrial production of quinoa protein with desired quality.