About 90% of the world’s natural gas hydrates (NGH) exist in deep-sea formations, a new energy source with great potential for exploitation. There is distance from the threshold of commercial exploitation based on the single well currently used. The complex structure well is an efficient and advanced drilling technology. The improvement of NGH productivity through various complex structure wells is unclear, and there is no more complete combing. Thus, in order to evaluate their gas production characteristics, we establish a mathematical model for exploitation of NGH, and then 13 sets of numerical models based on the geological parameters of the Nankai Trough in Japan are developed and designed, including a single vertical well, a single horizontal well, 1~4 branch vertical wells, 1~4 branch horizontal wells, and 2~4 branch cluster horizontal wells. The research results indicate that wells with complex structures represented by directional wells and multilateral wells can significantly increase the area of water and gas discharge, especially cluster wells, whose productivity can be increased by up to 2.2 times compared with single wells. Complex structural wells will play an irreplaceable role in the future industrialization of NGH.