The physicochemical properties of cyanidin-3-O-glucoside (C3G) were investigated after binding with pectin from different sources (apple and peach) and fractions (water-soluble fraction (WSF), chelator soluble fraction (CSF) and sodium carbonate soluble fraction (NSF)). Apple WSF and peach CSF were high esterification degree pectin (DE) (63.23% and 55.66%). CSF of both AP and PP was abundant in HG and exhibited a much more linear structure than WSF and NSF. The maximum binding percentage was obtained at pH 2.0 for apple pectin (AP) (46%–50%) and at pH 3.5 for peach pectin (PP) (50%–54%). Binding with both pectins increased the color stability of C3G at pH 2.0. High DE pectin increased C3G light stability by reducing the degradation rate (0.03 h−1) compared to C3G alone (0.05 h−1). All the pectins reduced the thermal degradation rate of C3G, thus exhibiting a protective effect. A negative correlation was found between the relative RG I area and the particle size of the pectin-C3G complexes. Pectin played a leading role in the ζ-potential change.