Integrated multi-trophic aquaculture (IMTA) uses co-products of one species that are automatically recycled as an input for other species to get a high profit. Considering IMTA, a vertical intensification of mud crab (Scylla olivacea) fattening was carried out at the pond's bottom and in the floated cages. Genetically Improved Farmed Tilapia (GIFT) strain of Oreochromis niloticus was integrated with crabs in the free pond areas to increase farm output. The experiment was designed with three different treatments, such as crab stocked in earthen ponds (T1), crab stocked in earthen ponds with floated crab cages (T2), and crab stocked in earthen ponds with the integration of floated crab cages and GIFTs (T3). Water quality was monitored regularly to keep the parameters (i.e., temperature, salinity, water pH, dissolved oxygen, alkalinity, and ammonia) within the optimum range for aquatic organisms. The survival rate of crab was significantly higher in T2 and T3 compared with T1. In addition, T2 and T3 were also significantly higher in crab production than T1. Crab productions in the ponds were significantly lower than productions in the floated cages. Besides, the tilapia growth was also found consistent with a moderate survival rate in two consecutive years. Hence, the multi-trophic culture system supports farming mud crab and tilapia combinedly. This study advocates starting IMTA at a large scale at different crab farms. Moreover, some other high-value species may be considered for future research in addition to GIFTs.