The invention relates to a production method of a heavily phosphorus-doped thin substrate silicon epitaxial layer for Schottky devices. The method adopts a normal-pressure flat plate type epitaxial furnace, and comprises the following steps: 1, polishing the pedestal of the epitaxial furnace at a high temperature by using hydrogen chloride with the purity being not lower than 99.99%; 2, filling the epitaxial furnace with a phosphorus-doped silicon substrate slice, and sequentially purging the cavity of the epitaxial furnace by nitrogen and hydrogen, wherein the purities of nitrogen and hydrogen are not lower than 99.999% respectively; 3, polishing the surface of the silicon substrate slice by using a hydrogen chloride gas; 4, purging the surface of the silicon substrate slice by using a bulk flow of hydrogen; 5, growing an intrinsic epitaxial layer; 6, carrying out variable flow purging on the reaction cavity of the epitaxial furnace; and 7, growing a doped epitaxial layer. The thickness inhomogeneity of the epitaxial layer is smaller than 1%, the resistivity inhomogeneity of the epitaxial layer is smaller than 1%, the surface of the epitaxial layer has no stacking fault, dislocation, slip lines, mist or other defects, the width of a transition region under optimum conditions can be smaller than 1[mu]m, and requirements of the silicon epitaxial layer by the Schottky devices can be completely met, so the performances and the yield of the Schottky devices are improved.