Information system audit is a product of combining both information technique and audit. Its generalized application can normalize the running of information system for various industrial department over whole life circle under the condition of high speed development, reduce information risk,and also guarantee profit to enterprise.Aiming at the different understanding on ISA generally used in China,we analyze and compare the difference between ISA and CAA(computer assisted audit),such as meaning,object,content,technique,method and operator,and so on.The paper shows that both ISA and CAA should be developped in audit field,that ISA is a new kind of audit to be different from CAA,and that there exists some disadvantage by means of computer audit summarizing CAA and ISA,so it is necessary to speed up to develop ISA.