This study aims to explore the design and development process of the Matter module for secondary school students. The needs analysis shows a similar perception between students and teachers who described the matter topic as complex due to the abstract nature of the Matter topic. This module emphasises the use of animation in visualising particles in different matter states. The module was designed to make learning more active and meaningful by integrating computational thinking skills through cooperative and project-based learning. Through this approach, students are actively involved in building animation projects to visualise the movement of particles by applying computational thinking concepts (abstraction, decomposition, generalisation, algorithm, and evaluation) as they engage with programming in Scratch. Thus, to systematically design and develop the Matter module, the ADDIE model was employed. The design and development of the module comprise five phases, Analysis, Design, Development, Implementation, and Evaluation. The module was evaluated by experts using a formative evaluation approach. The results show that the validity of the Matter module is high and can support the integration of computational thinking skills.