An exemplary inner substrate for manufacturing multilayer printed circuit boards is provided. The inner substrate has a number of substrate units and a number of transverse folding portions alternately arranged along a longitudinal direction of the inner substrate. Each of the substrate units is configured for forming a unitary printed circuit board. Each of the folding portions is interconnected between neighboring substrate units. Each of the folding portions defines at least one line weakness perpendicular to the longitudinal direction of the inner substrate for facilitating folding and unfolding the neighboring substrate units to each other. An exemplary method for manufacturing multilayer printed circuit boards using the inner substrate is also provided. The method can improve efficiency of manufacturing multilayer printed circuit boards.