The invention discloses a gene sequence analysis apparatus with an intelligent comparison function. According to the gene sequence analysis apparatus, four parts of a gene library server, a sequence comparison module, an intelligent comparison module and a health analysis module are designed for gene libraries stored in various treatment devices of a hospital; a certain number of standard use case genes are used as a standard gene sequence; a gene sequence of a user is compared with the standard gene sequence through certain comparison generation; a similarity result is analyzed to obtain a conclusion that the user has a sub-healthy or unhealthy possibility; production and life guidance is given; the user can perform intelligent comparison with a good friend to obtain a winning or losing result; and a potential gene sub-healthy probability of the user is prompted friendly through an intelligent comparison result to attract the attention of the user.