The present disclosure relates to a semiconductor structure and a manufacturing method thereof. The method of manufacturing a semiconductor structure includes: providing a base; forming a plurality of first trenches arranged in parallel at intervals and extending along a first direction, and an initial active region between two adjacent ones of the first trenches, wherein the initial active region includes a first initial source-drain region close to a bottom of the first trench, a second initial source-drain region away from the bottom of the first trench, and an initial channel region located between the first initial source-drain region and the second initial source-drain region; forming a protective dielectric layer, wherein the protective dielectric layer covers a sidewall of the second initial source-drain region and a sidewall of the initial channel region; thinning the first initial source-drain region.