Ultrathin two-dimensional (2D) layered transition metal dichalcogenides (TMDs) have attracted considerable attention owing to their unique properties and great potential in a wide range of applications. Great efforts have been devoted to the preparation of novel-structured TMD nanosheets by engineering their intrinsic structures at the atomic scale. Until now, a lot of new-structured TMD nanosheets, such as vacancy-containing TMDs, heteroatom-doped TMDs, TMD alloys, 1T'/1T phase and in-plane TMD crystal-phase heterostructures, TMD heterostructures and Janus TMD nanosheets, have been prepared. These materials exhibit unique properties and hold great promise in various applications, including electronics/optoelectronics, thermoelectrics, catalysis, energy storage and conversion and biomedicine. This review focuses on the most recent important discoveries in the preparation, characterization and application of these new-structured ultrathin 2D layered TMDs.