A substrate heat treatment apparatus for heat-treating a substrate includes a bake plate for supporting the substrate, and a cover disposed above the bake plate and temperature-controlled for securing a heat-treating atmosphere of the bake plate. An adjusting device adjusts a space between the cover and the bake plate. A control device adjusts the space, through the adjusting device, successively to a transport space for allowing transport of the substrate, a transitional space smaller than the transport space and close to the bake plate, and a steady space smaller than the transport space and larger than the transitional space.