The invention discloses a manufacturing method of a printed circuit board substrate with low roughness on a copper surface. The manufacturing method comprises the following steps: firstly, carrying out hot pressing solidification on a prepreg, covering a piece of release paper on the prepreg subjected to the hot pressing solidification, laminating, and then tearing off the release paper, so that a copper-free substrate is produced; secondly, depositing a first thin copper layer on the copper-free substrate; thirdly, making a light sensation membrane provided with patterns on the first thin copper layer by adopting a light sensation membrane image transfer method; fourthly, plating a second copper layer by adopting an electroplating method; fifthly, removing the light sensation membrane, and removing the first thin copper layer in a rapid etching manner, so that only a high-resolution pattern circuit coating is left. The invention provides a manufacturing method of a printed circuit board substrate with low roughness on the copper surface, so that signal stability of a printed circuit board is improved, and good dimensional stability during final lamination is realized.