The formation mechanisms and properties of thermally induced canola protein gels were investigated over a broad range of pHs (5–11) and processing temperatures (80–120 °C) involving two canola protein fractions, CP1 and CP2 with napin and cruciferin as major component, respectively. The protein conformation changes and interactions during gel formation were monitored by Fourier-transform infrared spectroscopy and advanced rheometer, and the protein network microstructures were observed using scanning electron microscopy. The results revealed that CP1 and CP2 exhibited different thermal and gelling properties due to their distinct molecular weight and amino acid composition. However, for both of them, lower heating temperature and pH only caused protein denaturation without splitting of disulfide bonds to produce randomly aggregated particulate fractal microstructure which was mainly stabilized by hydrophobic interactions. Whereas new gels with macro-porous dense wall structure and dramatically improved mechanical strength were prepared at high heating temperature and pH due to establishment of bridges between the interaction points on molecular chains. This generated knowledge has allowed preparation of canola protein gels with modulated mechanical properties by controlling the processing conditions, thus provided opportunities for canola protein to be used as new gelling reagent in both food and non-food applications.