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.