A manufacturing method of a via-hole connection structure, a manufacturing method of an array substrate and an array substrate are provided by the embodiments of the present disclosure, and the manufacturing method of the via-hole connection structure includes: forming an insulation layer on a base substrate and forming a first via hole in the insulation layer; forming a connection portion in the first via hole; forming a protection layer covering the connection portion on a surface of the insulation layer; forming a second via hole in the insulation layer and in the protection layer; removing at least a portion of the protection layer to expose the connection portion.