The invention provides a manufacturing method of a semiconductor structure. The method includes the steps of step 1, providing an SOI substrate and forming a heavy doping buried layer and a surface active layer on the substrate, step 2, forming a grid pile and a side wall on the substrate, step 3, forming an opening in one side of the grid pile, wherein the opening penetrates through the surface active layer and the heavy doping buried layer and stops in a silicon film above an insulation buried layer of the SOI substrate, step4, filling the opening to form a backfill plug, and step 5, forming a source region / drain region, wherein the source region and the heavy doping buried layer are overlapped, and partial drain region is placed in the backfill plug. Correspondingly, the invention further provides the semiconductor structure. According to the semiconductor structure and the manufacturing method thereof, the heavy doping buried layer is beneficial to reducing the width of a source region depletion layer / a drain region depletion layer and restricting the short-channel effect; the heavy doping buried layer and the source region are overlapped to form heavy doping pn junctions, therefore, the floating body effect of SOI MOS devices is effectively restricted, semiconductor device performance is effectively improved, leading out on regions is not needed, and the area and cost of devices are saved.