A method for manufacturing a semiconductor apparatus, comprising: providing a semiconductor substrate (31, 41); forming a dielectric layer (32, 42) on the semiconductor substrate (31, 41); forming a functional layer (33, 43) on the dielectric layer (32, 42), wherein the functional layer (33, 43) is capable of reacting with oxygen; forming a hard mask layer (34, 44) on the functional layer (33, 43); patterning the semiconductor substrate (31, 41) to form an opening (36, 46) on the semiconductor substrate (31, 41), wherein the opening (36, 46) goes through the hard mask layer (34, 44) and the functional layer (33, 43) and extends into the dielectric layer (32, 42); performing an oxidization process on side surfaces of the functional layer (33, 43) inside the opening (36, 46) to form oxide layers (37, 47); and performing a first process on the semiconductor substrate (31, 41), wherein the first process comprises: removing a portion of the dielectric layer (32, 42) that is underneath the opening (36, 46) to expose the semiconductor substrate (31, 41); and removing the oxide layers (37, 47) on the side surfaces of the functional layer (33, 43) to form a contact hole (38, 48), wherein a first portion of the contact hole (38, 48) is in the functional layer (33, 43), a second portion of the contact hole (38, 48) is in the dielectric layer (32, 42), the width of the first portion of the contact hole (38, 48) is larger than the width of the second portion of the contact hole (38, 48). providing a semiconductor substrate (31, 41); forming a dielectric layer (32, 42) on the semiconductor substrate (31, 41); forming a functional layer (33, 43) on the dielectric layer (32, 42), wherein the functional layer (33, 43) is capable of reacting with oxygen; forming a hard mask layer (34, 44) on the functional layer (33, 43); patterning the semiconductor substrate (31, 41) to form an opening (36, 46) on the semiconductor substrate (31, 41), wherein the opening (36, 46) goes through the hard mask layer (34, 44) and the functional layer (33, 43) and extends into the dielectric layer (32, 42); performing an oxidization process on side surfaces of the functional layer (33, 43) inside the opening (36, 46) to form oxide layers (37, 47); and performing a first process on the semiconductor substrate (31, 41), wherein the first process comprises: removing a portion of the dielectric layer (32, 42) that is underneath the opening (36, 46) to expose the semiconductor substrate (31, 41); and removing the oxide layers (37, 47) on the side surfaces of the functional layer (33, 43) to form a contact hole (38, 48), wherein a first portion of the contact hole (38, 48) is in the functional layer (33, 43), a second portion of the contact hole (38, 48) is in the dielectric layer (32, 42), the width of the first portion of the contact hole (38, 48) is larger than the width of the second portion of the contact hole (38, 48). removing a portion of the dielectric layer (32, 42) that is underneath the opening (36, 46) to expose the semiconductor substrate (31, 41); and removing the oxide layers (37, 47) on the side surfaces of the functional layer (33, 43) to form a contact hole (38, 48), wherein a first portion of the contact hole (38, 48) is in the functional layer (33, 43), a second portion of the contact hole (38, 48) is in the dielectric layer (32, 42), the width of the first portion of the contact hole (38, 48) is larger than the width of the second portion of the contact hole (38, 48).