Abstract: This paper studies the computing experiment methodology of the Parallel Experiment Theory(PET) after summarizing the PET's fundamental concepts, then proposed the 3-layered computing experiment methodology: factor experiments, system experiments and System-of-Systems experiments, after which the specific requirements of experiments is provided, the executive scheduler methods of the computing experiments is researched, and the basic idea and available technologies is addressed for the computing experiments' application. Ultimately, the main tasks of PET's application from 3 aspects are discussed, which are, respectively, the development of the artificial system environment, the integration and application of the ranges' experiment data sources, and the physical system in loop computing experiments.