Present invention provides a method of holding substrate and a substrate holding system where the amount of foreign substances on the back surface can be decreased, and a little amount of foreign substances may be transferred from a mounting table to a substrate. The substrate holding system comprises a ring-shaped leakage-proof surface having smooth surface on the specimen table corresponding to the periphery of the substrate, a plurality of contact holding portions against the substrate on the specimen table between the corresponding position to the periphery of the substrate and the corresponding position to the center of the substrate, and electrostatic ttraction means for fixing the substrate by contacting the back surface of the substrate to the ring-shaped leakage-proof surface and the contact holding portions. The substrate contacts to the cooling surface at the ring-shaped leakage-proof surface and the contact holding portion placed on a position inside the ring-shaped leakage-proof surface. The back surface of the substrate and the cooling surface do not contact to each other in the large portion of the remaining area.