The invention discloses a preparation method for a gill tissue paraffin section. The preparation method comprises the following steps: fixing, decalcifying, dehydrating, transparentizing, carrying out paraffin permeation, embedding, slicing, sticking sections, expanding the sections, de-waxing and rehydrating, staining, re-staining, sealing and the like. Compared with an existing paraffin section manufacturing method, an operation process of dehydrating, transparentizing and immersing by wax is improved; the preparation fixing and tissue wax immersing effects of gill tissue paraffin are improved; a slicing problem when the gill tissue paraffin section is prepared is improved; the structure definition of the gill tissue section is greatly improved; a plurality of problems in a gill tissue manufacturing process in the prior art are solved. The preparation method is good for antigen positioning of immunocytochemical staining, so that when experiments including in-situ hybridization, immunohistochemistry, immunofluorescence and the like are carried out on the gill tissue paraffin section, tissue distribution and cell positioning of some genes and proteins can be displayed, and further feasible conditions are provided for carrying out gill research on levels of cells, genes and proteins.