The invention discloses a preparation method of an immobilized 
microorganism embedding 
microsphere for restoring a riverbed bottom mud 
ecosystem. The preparation method comprises the steps of PVA (
polyvinyl alcohol) 
gel preparation, cross-linking agent preparation and 
microsphere preparation, wherein the PVA 
gel preparation comprises the steps of preparing a PVA solution with a concentration of 8-10%, adding embedding agents to the PVA solution, namely 
sodium alginate with a concentration of 0.5-2%, 
calcium carbonate with a concentration of 0.2-0.5%, 
silicon dioxide with a concentration of 2.0-4.0%, and 300-500 mesh attapulgite 
powder or 300-500 mesh 
activated carbon powder with a concentration of 0.5-1.0%, and adding activated limon 
microorganism bacterium liquid with a concentration of 10-15%; and the 
microsphere preparation comprises the steps of dropwise adding PVA gel to a 
calcium chloride saturated 
boric acid solution, stirring, obtaining immobilized 
microorganism activated spherular particles with the particle size of 3-5mm, conducting immobilized crosslinking for 24-36h at 4-8 DEG C, taking out, and washing with normal 
saline. Compared with the prior art, the microsphere can remove 
total organic carbon and 
total nitrogen in riverbed bottom mud effectively, and can improve COD (
chemical oxygen demand), 
ammonia nitrogen and 
total nitrogen pollution conditions of an overlying 
water body of the bottom mud, and the preparation method is an ecological riverway management scheme which is efficient, low-consumption and simple to operate, and has a development prospect.