A thin heat pipe structure includes a pipe body, a thin-sheet member, and a plurality of bosses. The pipe body internally defines a receiving space, in which a working fluid is provided. The thin-sheet member includes a plurality of open spaces, and the bosses are provided in the open spaces, so that the bosses and the thin-sheet member are disposed in the receiving space of the pipe body at the same time. A method of manufacturing thin pipe structure is also disclosed for manufacturing thin heat pipe structure with reduced time and labor, and protecting a wick structure formed in the thin heat pipe structure against damage. Therefore the thin heat pipe structure can be manufactured with increased good yield and at reduced manufacturing cost.