The understanding of the evolution mechanism of thiolate-protected Au nanoclusters from the homoleptic Au(I)-SR clusters to core-stacked ones is crucial for the synthesis of novel thiolated Au clusters. In this work, the global search for a series of "intermediate" Au-m(SR)(n) clusters with m and n ranging from 5 to 12 was implemented by combining basin hopping algorithm, genetic algorithm, and density functional theory (DFT) calculations. Most of Au-m(SR)(n) clusters possess the core shell structure. Specifically, some typical topologies, such as tetrahedral Au-4, triangular bipyramid Au-5, octahedral Au-6, and vertex-shared Au-7, are found to be dominant within the inner core of various clusters. Along with the increase in the number of gold atoms and thiolates, the preliminary nucleation and growth processes of both inner-core and staple-motif protecting units are grouped into three kinds of size evolution routes, i.e., core growth, core dissolution, and staple-motif growth, respectively. Some metastable isomers may also play an important role in the evolution of clusters. The core structures in the lowest-lying isomers and some metastable isomers are similar to the intact or part of the cores found in experimentally detected species. Both the lowest-lying and metastable intermediate clusters may serve as the building block for the further growth. These results rationalize the preliminary nucleation in the "reduction growth" stage, shedding light on the size-evolution mechanism of RS-AuNPs.