A new approach to improve the light-emitting efficiency of Ge(Si) quantum dots (QDs) by the formation of an ordered array of QDs on a pit-patterned silicon-on-insulator (SOI) substrate is presented. This approach makes it possible to use the same pre-patterned substrate both for the growth of spatially ordered QDs and for the formation of photonic crystal (PhC) in which QDs are embedded. The periodic array of deep pits on the SOI substrate simultaneously serves as a template for spatially ordering of QDs and the basis for two-dimensional PhCs. As a result of theoretical and experimental studies, the main regularities of the QD nucleation on the pre-patterned surface with deep pits were revealed. The parameters of the pit-patterned substrate (the period of the location of the pits, the pit shape, and depth) providing a significant increase of the QD luminescence intensity due to the effective interaction of QD emission with the PhC modes are found.