The present invention discloses a method of fabricating dual trench isolated epitaxial diode array. This method starts with the formation of heavily-doped first conductivity type regions and heavily-doped second conductivity type regions on the substrate, followed by epitaxial growth, then the formation of the isolations between diode array word lines by deep trench etch and the formation of the isolations between bit lines vertical to deep trenches by shallow trench etch, and finally the formation of separate diode array cells in the regions enclosed by deep and shallow trench isolations by ion implantation. This invention also provides a method of preventing the crosstalk current between adjacent word lines and bit lines of epitaxial diode arrays isolated by foregoing dual shallow trenches. This invention can be used for diode-driven, high-density, large-capacity memory, such as phase change random access memory, resistive memory, magnetic memory and ferroelectric memory; the method thereof is completely compatible with conventional complementary metal-oxide semiconductor (CMOS) process, and because the diode arrays can be formed before the formation of peripheral circuits, no drift of peripheral circuits will be caused by the thermal process thereof, thereby solving the technical challenge of fabricating high-density, large-capacity embedded phase change random access memory.