An object of this invention is to properly identify or manage mask blank substrates, mask blanks, and so on. A manufacturing method of a mask blank substrate (10) includes a substrate preparing step of preparing a plate-like substrate with a square main surface (102), and a marker forming step of forming a marker (106a to 106d) for identifying or managing the substrate on each of at least a plurality of end faces among four end faces (104a to 104d) of the substrate. The four end faces are continuous with sides of the main surface, respectively.