Provided are a method for polishing a silicon substrate according to which PID can be reduced and a polishing composition set usable in the polishing method. The silicon substrate polishing method provided by this invention comprises a stock polishing step and a final polishing step. The stock polishing step comprises several stock polishing sub-steps carried out on one same platen. The several stock polishing sub-steps comprise a final stock polishing sub-step carried out while supplying a final stock polishing slurry PF to the silicon substrate. The total amount of the final stock polishing slurry PF supplied to the silicon substrate during the final stock polishing sub-step has a total weight of Cu and a total weight of Ni, at least one of which being 1 μg or less.