Abstract: The detection efficiency of thermal neutron and deposited energy spectrum for various structures of three-dimensional square pore silicon detector with ⁶LiF used as a neutron conversion material were simulated with Geant4 program based on Monte-Carlo method. The influence of pore parameter on detection efficiency was studied in detail. The pore size, pore space, pore depth and the lowest limit of detection (LLD) were employed to discuss the change of detection efficiency of thermal neutron. The results show that the detection efficiency increases at first and then decreases with increase of pore size or pore space, while it increases constantly to an extreme with pore depth. When the LLD is 300 keV, the detection efficiency of three-dimensional square pore silicon detector with pore space more than 6 μm is less affected by LLD. In theory, the three-dimensional square pore silicon detector with pore space of 6 μm, pore size of 30 μm and pore depth of 1 mm achieves the highest detection efficiency of 59.5%.