Time and space are fundamental concepts for characterizing and understanding our world. Despite of continuous curiosity and extensive studies, the nature of time and space remains elusive, and the underlying quantum structure is unclear. Here we propose a molecular model based on energy space decomposition to incorporate time and space synthetically in a unified framework. In the proposed model, the multipole expansion of action mapped to energy modules in scalar, vector, and matrix forms, results in the generators of time, space, and a material framework, cloud. And the invariance of time, space and cloud transformation corresponds to the conservation of energy, momentum, and mass, respectively. The classification of energy modules reveals a periodicity of energy elements, which constructs a hierarchical world in a molecular framework with dynamics represented by energy transformations. Here the role of time and space could switch from each other, and motion is attributed to the coupling of particle with intermediate bosons, corresponding to energy transformations among different energy modules. The application on Bohr model demonstrates that this picture provides a consistent classical interpretation to the foundation of quantum mechanics, and suggests an atomic model for gravitation.