The invention discloses a method for obtaining natural horseshoe crab fertilized eggs by building a pool bottom overhead, laying sand and conducting partition. The method is characterized by including the steps of firstly, selecting parent horseshoe crabs, wherein three or more pairs of parent horseshoe crabs are selected as the parents in the mating season each year; secondly, refitting a parent horseshoe crab pool indoors, wherein the pool bottom of a breeding pool is built overhead through a wood frame, a 60-mesh bolting-silk net is laid on the pool bottom, an oxygen pipe used for inflation is arranged in the overhead wood frame, and sand is laid on an egg laying area; thirdly, breeding the parent horseshoe crabs indoors, wherein the parent horseshoe crabs selected in the first step are placed in the parent horseshoe crab pool refitted in the second step, and indoor inflation breeding is conducted; fourthly, making the parent horseshoe crabs lay eggs and release semens, wherein the parent horseshoe crabs can lay eggs and release semens in 2 days to 10 days after entering the breeding season to form fertilized eggs; fifthly, sieving and washing the fertilized eggs; wherein after the fertilized eggs are hardened, the fertilized eggs and sand are dug out, elutriation is conducted through a screen with the diameter of 2 mm, all the sand is leaked out, and the fertilized eggs are left. Different from a method for obtaining the fertilized eggs by killing horseshoe crabs, the method has the advantages that a large number of high-quality fertilized eggs can be obtained, and the method is easy and convenient to operate, efficient, highly feasible and the like.