Born in 1808 in Orono, Maine, Jonathan Norcross was the second son of clergyman Jesse Norcross, a Baptist minister from Penobscot, and his wife Nancy (née Gaubert) from Dresden, Maine. He had six siblings, including older brother Nicholas Gaubert Norcross ("see last section below"). His younger siblings include: Livonia (b. Jan. 1810), brother Jesse (b. 3 Jun. 1812), Nancy Gaubert (b. 2 Mar. 1816), who married Moses M. Swan of Augusta, Maine; Maria (b. Feb. 1818), and Louisa Norcross (b. Oct. 1823). After the passing of Nancy, his second wife was Mary Ann Hill.