The invention provides a method for designing a structure of a modularized analytical instrument system, and belongs to the field of designing and manufacturing of analytical instruments. In the method, the functions of the analytical instrument are divided into a plurality of independent modules, and the modules form a set of analytical instrument system in a distributed and loose coupling mode, wherein the modules fall into a scheduling module and a functional module which are of data interaction by a bus and in a mode of peer-to-peer communication. The method has the advantages of improving reusability and interchangeability of modules between the analytical instruments, saving cost of R&D, production, manufacturing and maintenance, simultaneously lowering system complexity, strengthening system expandability and facilitating development, integration and maintenance of analytical instrument systems.