Currently, systems for automating scientific calculations are being actively developed, the use of which makes it possible to carry out calculations using high-performance resources, control the parallel execution of an application in a distributed computing environment, and carry out multivariate calculations. The paper deals with the issues of building automation systems for scientific services for multi-scale modeling of composite materials. The presented methods, typical architecture and software tools make it possible to integrate the author’s software module or application software package into a platform for multi-scale modeling of composite materials with little effort. The constructed software solutions can be used to speed up and reduce the cost of searching for new composite materials with desired properties.