A substrate processing apparatus includes a robot having: an end effector, a first link structure including a fixing portion having a front end to which the end effector is fixed, a support portion, and a first hole formed in the support portion, a second link structure including a second hole, and a shaft inserted into the first and second holes, the shaft including an upper end having a height equal to or smaller than a height of the substrate mounted on the end effector; a vacuum transfer chamber, wherein the robot is installed in the vacuum transfer chamber; at least one process chamber disposed adjacent to the vacuum transfer chamber and configured to thermally process the substrate transferred from the vacuum transfer chamber by the robot; a module including one or more process chambers; and a cooling mechanism installed above the first link structure or the shaft.