Mangrove forests are facing the challenges of continual losses and unsustainable use globally. Ways to conserve and use mangrove ecosystems wisely are still largely unknown. In this study, a design to transfer traditional shrimp ponds to mangrove wetland eco-farms and restore mangroves for carbon accumulation was examined for ecosystem service benefits. In Shijiao Station, Fangchenggang City, Guangxi, the conversion of unused aquaculture ponds to mangroves served to increase carbon (C) storage by about 3.90 Mg C/year (with 0.92 Mg C/year of biomass C and 2.98 Mg C/year in soil) over an area of 1.95 ha. The net C stock change rates were 0.469 and 1.53 Mg C/ha/year in vegetation and soil, respectively, when converting from traditional shrimp ponds to mangrove eco-farms. This eco-farm system has been operational for 10 years, and, in addition to C sequestration value gained, provides economic values in aquaculture products ranging from 675–1,125 kg/ha/year. Such aquacultural systems could deliver 342/569 Mg/year in aquacultural products, accounting for 87–145 million CNY/year if just one-quarter of the unused ponds in Pearl Bay of Fangchenggang City were converted to mangrove eco-farms using the same design. In addition to the multiple ecological roles, including C sequestration value, that healthy mangrove ecosystems provide within an eco-farm, this approach can compensate the local economy from such land use change by converting to higher economic benefits. Mangrove eco-farms in Guangxi may also provide a new and sustainable approach (and incentive) for restoring mangroves.