The invention discloses a bioremediation nutritional agent for a water balance system and a preparing method thereof. The bioremediation nutritional agent comprises an algae component, a water-aqua microorganism component and a nutrient granule and powder component. The algae component comprises chlorella and plant cytokinin added to the chlorella; the water-aqua microorganism component comprises photosynthetic bacteria, saccharomycetes, lactic acid bacteria, composite bacilli, streptococcus faecalis, clostridium butyricum, bdellovibrio bacteriovorus and ferment; the nutrient granule and powder component comprises phosphorus pentoxide, rare earth, silicon earth, organic fermentation substances and a potentiating agent. The preparing method includes the steps of preparing the algae component, preparing the water-aqua microorganism component and preparing the nutrient granule and powder component. According to the bioremediation nutritional agent and the preparing method thereof, due to the theory of the yin and yang balance rule, under the effect of beneficial monodus subterraneus and beneficial microorganisms, rotten water plants are effectively decomposed, the nitrogen-and-phosphorus-balanced conversion function is achieved, dissolved oxygen of a water body is increased, the metabolism immunologic function of water products is improved, breeding cost is greatly reduced, and the ecological circulation water environment is formed.