The present application provides a method of manufacturing a semiconductor structure and a semiconductor structure. The method of manufacturing a semiconductor structure includes: forming a first conductive layer in a first trench of a substrate, where a top surface of the first conductive layer is recessed; forming a bit line structure on the first conductive layer; forming a third dielectric layer and a fourth dielectric layer, where the fourth dielectric layer at least covers the bottom and a side wall of a second trench; and removing a part of the first dielectric layer and the fourth dielectric layer that covers the bottom of the second trench, to form a third trench, where the third trench exposes the substrate. The semiconductor structure is manufactured through the method of manufacturing a semiconductor structure.