There are great differences between the current operation situation of the comprehensive bonded zone and the bonded logistics center in Hunan Province. In the aspects of service function, industry orientation, service area, etc., comprehensive bonded areas and bonded logistics centers have their own focuses and directions, but there are also some problems in the operation and development of bonded logistics in Hunan Province, such as functional coincidence, intensifying competition, and large individual gap. The main operational and development issues of bonded logistics in Hunan Province are overlapping of functions, intensification of competition, and large gap between individuals, and so on. The development is extremely unbalanced, the customs declaration is cumbersome, and the operation is not smooth. Restrictive factors of bonded logistics' development in Hunan are that the economic development in the province is out of balance, the industrial competitiveness is not strong, the location advantage is weak, the dependence on foreign trade is low, the policy is upside down, and the utility of bonded logistics is reduced. The competition between the surrounding provinces and cities is fierce. It is proposed to rationally plan the distribution of business functions, to avoid excessive competition, to break the interests of departments, to promote the coordinated development of Hunan bonded logistics, and to optimize customs clearance procedures. The countermeasures and suggestions like reducing the “second customs declaration” and strengthening the management of investment promotion projects are put forward to promote the development of bonded logistics in Hunan Province.