Many portable devices such as soldier carrying devices are powered by low-weight but high-capacity lithium ion (Li-ion) batteries. An effective battery thermal management (BTM) system is required to keep the batteries operating within a desirable temperature range with minimal variations, and thus to guarantee their high efficiency, long lifetime and great safety. However, the rigorous constraints imposed by the budgets in weight and volume for this specific application eliminate the possible consideration of many existing classical cooling approaches and make the development of BTM system very challenging in this field. In this paper, a flexible hydrogel-based BTM system is developed to address this challenge. The proposed BTM system is based on cost-effective sodium polyacrylate and can be arbitrarily shaped and conveniently packed to accommodate any Li-ion stacks. This BTM system is tested through a series of high-intensity discharge and abnormal heat release processes, and its performance is compared with three classical BTM systems. The test results demonstrate that the proposed low-cost, space-saving, and contour-adaptable BTM system is a very economic and efficient approach in handling the thermal surge of Li-ion batteries.