The invention provides a semiconductor structure and a manufacturing method thereof. The manufacturing method comprises the following steps: S1, providing a substrate; S2, forming an induction structure on the surface of the substrate; S3, arranging a first block copolymer layer on the exposed surface of the substrate, and heating the first block copolymer layer for the first time to form a firstpre-split-phase structure layer comprising a first pre-block and a second pre-block; S4, forming at least one second split-phase structure layer on the surface, far away from the substrate, of the first pre-split-phase structure layer; S5, at least removing the fourth block, the second block and part of the substrate in sequence to form the substrate with a predetermined pattern; S6, at least removing the first block, the third block and the induction structure above the remaining substrate. According to the manufacturing method, a phase splitting process is carried out twice, and the manufactured structure has fewer defects, is better in uniformity and is lower in edge roughness.