Provided are a semiconductor device capable of detecting a light of each color with high accuracy without using a color filter, particularly enhancing detection accuracy of charges obtained by photoelectric conversion of a long-wavelength light, and manufacturing and control methods thereof. The semiconductor device has a p type semiconductor substrate, and first, second and third pixel regions. These regions each include a p type well region in the p type semiconductor substrate and an n type region configuring a pn junction therewith. The p type well region of the first pixel region is thinner, from the main surface to the lowermost portion, than that of the second and third pixel regions. On the side opposite to the main surface of the p type well region of the first and second pixel regions, a buried p type well region contiguous to the p type well region is further placed.