A substrate heat treatment apparatus for heat-treating a substrate includes a bake plate having projections on an upper surface thereof, a seal unit disposed peripherally of the upper surface of the bake plate for closing a lateral area of a minute space formed between a lower surface of the substrate and the upper surface of the bake plate when the substrate is placed on the bake plate, and exhaust bores for exhausting gas from the minute space. The substrate placed on the bake plate is heat-treated in a state of the gas exhausted from the minute space through the exhaust bores.