The convergence of technology and human creativity in Society 5.0 demands innovative approaches to address complex scientific challenges across diverse domains, making cohesive experiments essential. The increasing complexity, diversity, and scale of data, along with the need for interdisciplinary exploration and knowledge discovery, present significant challenges. Computational scientific experiments leverage methods such as data acquisition, preprocessing, analysis, and visualization to simulate and understand intricate phenomena. However, existing interactive environments (e.g., Jupyter Notebook, Google Colab), collaborative groupware systems (e.g., Co-Taverna, iPlant Collaborative), and scientific workflow management systems (e.g., Galaxy, Kepler) often fall short in providing the automation, scalability, and reproducibility required for scientific experimentation. Additionally, they lack the usability and flexibility necessary for accommodating varying skill levels among researchers and supporting effective collaboration across domains. This paper introduces a collaborative framework designed to support cross-domain computational scientific experiments, fostering automation of complex operations, intuitive workflow composition, easy collaboration among researchers, comprehensive data and process lineage management, and seamless integration of data, tools, and experiments, allowing domain experts to focus on scientific discovery rather than the technical complexities involved. This study outlines the architecture and key features of the framework and discusses the challenges it addresses for Society 5.0. As a proof of concept, we developed prototype workflow management systems for code clone analysis, bioinformatics, image processing, and machine learning by integrating tools and services from the respective domains. We conducted case studies illustrating the creation of numerous cross-domain workflows and evaluated the framework’s flexibility through tool integration via a user study. The results demonstrate its effectiveness in facilitating cross-domain scientific experimentation, aligning with the principles of Society 5.0, and fostering innovation and knowledge discovery across diverse scientific domains. Two anonymous virtual machines of the prototype are hosted at http://143.110.214.145 and http://165.22.229.234 for experimentation.