This paper presents a fabrication method of a two-dimensional (2D) diffraction grating with isolated photoresist pattern structures in order to reduce fluctuation in the grating pitch due to the thermal expansion. At first, theoretical calculations for the fabrication of a 2D diffraction grating with isolated photoresist pattern structures are carried out to estimate the influences of exposure and development time on the pattern structures to be fabricated through the pattern exposure and development process. A diode laser-based compact non-orthogonal two-axis Lloyd’s mirror interferometer system designed in a size of 500 mm × 840 mm is then built on a breadboard for stable mask-less interference lithography. Basic performances of the newly developed compact interferometer system are evaluated through the fabrication of 2D diffraction gratings to demonstrate the feasibility of the theoretical calculations and the developed lithography system.