Objective To explore a simple method to replace absolute ethanol and xylene with n-butanol for preparation of sections of whole rat embryos at different gastational ages. Methods Embryonic day (E) 14, 16, 18, 20 rat embryos were collected and fixed. After dehydration in low concentrations of the ethanol, some embryos were treated with the traditional absolute ethanol-xylene method in which absolute ethanol and xylene were used for dehydration and clearing, and other embryos were further dehydrated and cleared with the n-butanol method. Then, all the embryos were embedded in paraffin, cut on a microtome, and stained with hematoxylin-eosin. The quality of embedded blocks and embryo sections was compared and evaluated. Results Compared with the absolute ethanol-xylene method for preparation of whole rat embryo sections, the n-butanol method was more simple, and easier to control the time in the whole processes. Moreover, the embryos treated with n-butanol had better cutting performance and higher quality in morphological preservation of the hepatic tissue. Conclusion As a simple, safe and reliable method, the n-butanol method can replace the absolute ethanol-xylene method for preparation of whole rat embryo sections.