Aquaponics is considered a new industrialized food production approach to meet the increasing needs of expanding urbanization. In this system, nutrient recovery from aquaculture sludge can achieve zero solid waste discharge and supplement nutrients to hydroponics system, which yield environmental and economic benefits. Anaerobic and aerobic mineralization are common approaches for the nutrient conversion of aquaculture sludge, but they are challenged by low-value products, nutrient loss, and large amounts of biomass by-products produced during the process. In this review paper, phototrophic bioconversion of aquaculture sludge by anoxygenic phototrophic bacteria (APB) is proposed to minimize carbon and nutrient dissipation, through which the resulting mineral nutrients can be taken up by plants and the assimilated protein-rich biomass can be utilized by aquaculture animals as food. Pre-treatment to solubilize aquaculture sludge is essential to obtain bioavailable substrates, because aquaculture sludge cannot be utilized by APB in the organic solid form. The characteristics of anaerobic and aerobic solubilization processes are discussed, and the performance of phototrophic bioconversion by APB under anaerobic and aerobic conditions is compared. A multi-loop aquaponic system with four ecological coupling models was developed for the recovery of APB-based nutrients. The symbiotic mechanism between the solubilization and phototrophic bioconversion process should be focused in the future.