The experiment was blastocyst and hatch blastocyst of ICR mouse culture in vitro, and the effect of two methods to the cell counting of mouse embryo was compared. Method 1 was that blastocyst and hatch blastocyst was pressed with the 0.5% low osmosis liquid of Sodium Citrate and Giemsa dye, and the treat time of low osmosis and dye of corresponding embryo was identical in different period;Method 2 was blastocyst and hatched blastocyst was pressed with Hematoxylin, and the treat time was different in different period.The results indicated that in method 2 the outline of mouse blastocyst and hatched blastocyst cell ball was clear, the cleft of cell was obvious, its rate of observation was 94.7% and 96.8% respectively; while in method 1 the cleft of embryo cell ball was unclear, and the outline of some cells was blurry, and its rate was 70.5% and 69.6% respectively.Method 2 is significantly better than method 1 by adopting count method of press of small mouse blastocyst and hatched blastocyst ( P0.05) .