Alkaline pH12 shift treatment performed at varying temperatures (20-80 °C for 1, 5, and 60 min) was applied to structurally modify hemp seed protein isolate (HPI). The solubility of HPI (∼20%) was remarkably improved ( p < 0.05) with elevating the temperature and prolonging the holding time, reaching 97.5% at 80 °C for 60 min. The treated HPI exhibited a strong tendency of forming soluble large aggregates. To limit lysinoalanine (LAL) production, heating was methodically controlled to 60 °C and 5 min, where the LAL content never exceeded 100 mg/100 g of protein and the loss of cysteine and lysine was also minimal. The emulsifying activity of HPI was improved by this mild pH shift-heating combination treatment as a result of the dissociation of protein subunits, unraveling of the tertiary structure, and exposure of hydrophobic groups. Moreover, the emulsion formed by the treated protein maintained a superior stability in particle size and distribution during storage.