A mobility header compression method and system for an IPv6-based LoWPAN is provided for supporting IPv6 mobility to the IPv6-based LoWPAN checks a packet carrying data and a first and a second headers containing transmission information about the data to determine whether the second header contains a compressed Internet Protocol version 6 (IPv6) information. When the second header contains a compressed IPv6 information, ands followed by a mobility header, a mobility support-indicative field of the first header is set to indicate that the second header is followed by the mobility header and the rest of the fields of the second header are compressed except for the mobility header-indicative field. A mobility information-indicative field of the mobility header is set to indicate inclusion of mobility information; and the rest of the fields of the mobility header are compressed except for the mobility information-indicative field.