Calcium chloride with final mass concentration of 0.05 g/L, 0.11 g/L and 0.22 g/L were added to mass concentration of 120 g/L ginkgo seed protein isolate (GSPI) and 5.0 g/L pectin (with two types of degree of esterification, which was 38% and 76%, respectively) composite solutions. The above prepared solutions were then heated to develop a GSPI/pectin composite gel. The determination of particle size and ζ-potential, rheology, texture profile analysis, protein electrophoresis, spectroscopic and microscopic techniques were employed to detect physiochemical characteristics of gel-forming solutions, gelling and functional properties of the resulting composite gels and their microstructure. The mode of action caused by calcium chloride was also prospected. The results indicated that calcium ions reduced the particle size of GSPI/pectin but not affected their electric charge, degraded rheological properties of the heat induced gels, formed a composite gel with a loosen structure. Accordingly, the textural propertied of the gels was weakened, whereas the water holding capacity was not significantly deteriorated. It was supposed that calcium ions impair the interaction between GSPI and pectin due to competitive binding to pectin and hence disrupt the balance of GSPI/pectin assembly. As the calcium concentration increased, the effects were notably prominent. The pectin with higher degree of esterification was more sensitive to calcium ions.