The invention provides a method and 
system for automatically designing a mouse breeding scheme based on the Mendel's genetic law. The method comprises the steps of building a breeding scheme model which comprises a 
project type, the number of genes contained in each breeding 
route, an identification mode, a 
mouse strain background and a background mouse age; inputting item information and startingand target mouse information, and generating at least one feasible breeding scheme, wherein the breeding scheme at least comprises the breeding 
route and required cost; and selecting and determiningthe breeding scheme. According to the method, the mouse breeding scheme 
design process and logic based on the Mendel's genetic law are immobilized and standardized and can be sorted according to certain logic, result errors caused by errors of designers can be avoided, and the optimal scheme is derived. The automatic design greatly improves the design efficiency of the breeding scheme, and can save a large amount of labor cost.