A heat treatment method includes a substrate holder that holds a plurality of substrates at predetermined vertical intervals and is carried into a heat treating furnace for performing a predetermined heat treatment on the substrates. The substrate holder has two holder constituting bodies each having a plurality of columns and substrate holding sections. One of the holder constituting bodies holds the substrates at a first, vertically adjacent distance so that their front surfaces face each other, while the other of the holder constituting bodies holds the substrates at a second, vertically adjacent distance so that their back surfaces face each other wherein the second distance is smaller than the first distance to ensure uniformity of the heat treatment. At least one of the holder constituting bodies moves in the vertical direction to change the positions of the holder constituting bodies relative to each other.