The invention provides a treatment method of a micro organ. The treatment method comprises the following step sequentially dialyzing a fixed micro organ in dialysate I for 2 to 5 days under 1 to 10 DEG C and in dialysate II for 4 to 8 hours under -40 to -15 DEG C, wherein a formula of the dialysate I comprises 1M of Tris alkaline solution which is prepared from 10 percent of Triton-X 100, 2 percent of BSA (Bull Serum Albumin) and 0.05M of NaCl, and the pH (Potential of Hydrogen) is 6.8; a formula of the dialysate II comprises ethanol and DMSO (Dimethyl Sulfoxide) which are 4 to 1 in volume ratio. The treatment method provided by the invention is used for carrying out sizing and whole permeation treatment on the micro organ, an original morphology of the micro organ is kept, and the purposeof enabling macromolecular matters to fully permeate each position without changing the structural morphology of the micro organ and tissue cells can be realized; the treated micro organ is capable of accurately and sensitively carrying out cellular or subcellular location and qualitative and relatively quantitative analysis on molecules on the micro organ by utilizing specific binding reaction of molecular matters and through corresponding observation means such as a fluorescent microscope. Aiming at the difficulties that internal organs of animalcules in the field of biology are very smalland a tissue section technique is difficult to implement for the internal organs, the method for researching in-vivo micro organ on molecular and cellular level is invented.