The invention discloses a nano-biological water body remediation agent for aquaculture and a preparation method thereof. The nano-biological water body remediation agent comprises a carrier and complex bacteria attached to the carrier, wherein the carrier comprises the following ingredients in percentage by weight: 10-70 wt% of nano tourmaline, 10-70 wt% of nano titanium dioxide, 10-70 wt% of modified zeolite and 10-50 wt% of montmorillonite, and the complex bacteria comprise photosynthetic bacteria, denitrifying bacteria, nitrifying bacteria and phosphorus accumulating bacteria. The nano-biological water body remediation agent for aquaculture, disclosed by the invention, is economical and environment-friendly and is simple and convenient to prepare; the adsorption characteristics of the natural mineral materials are cooperated with the degradation characteristics of the microorganisms, so that organics in a water body can be efficiently adsorbed and degraded, and the remediation efficiency of water quality is higher; and the microorganisms can increase the dissolved oxygen in the water body while harmful substances, such as ammonia nitrogen and hydrogen sulfide, are efficiently decomposed, excellent-quality baits can be supplied to aquatic livestock through the propagation of the microorganisms, and the secondary pollution on the water body cannot be caused.