The utility model relates to a method for large-scale preparation of cell microscopic samples, which comprises the following steps under sterile conditions: cover slips with ferrous powders are arranged in the microscopic hole of a microplate, or a metal gasket attractable by magnetism is positioned at the bottom of the microscopic hole in advance, and then the ordinary cover slips are arranged on the metal gasket; single cell suspension is arranged on the cover slips and cultured; when the growth of the cell meets the requirements, the culture fluid is sucked out, and the cell is washed; the biochemical reaction is conducted in the microscopic hole; when the reaction is completed, the cell is washed again; a magnetically attractable board is flatly arranged for holding the cover slips, and stationary liquid for the cover slips is applied on the glass slide, then the microplate is inversely arranged on the glass slide, thus the cover slips are shifted on the glass slide under the influence of the magnetic force of the magnetic board. By adopting the cover slips with ferrous powders or arranging the metal gasket which can be adsorbed by the magnetism at the bottom of the cover slips, all the cover slips are sucked out and shifted on the glass slider via the magnetic board. The utility model has the advantages of convenient operation and high efficiency.