The connection study between biological structure and function, as well as between anatomical data and mechanical or physiological models, has been of increasing significance with the rapid advancement in experimental physiology and computational physiology. The China Physiome Project (CPP) is dedicated in optimization of the connection exploration based on standardization and integration of the structural datasets and their derivatives of cryosectional images with various standards, collaboration mechanisms, and online services. The CPP framework hereby incorporates the three-dimensional anatomical models of human and rat anatomy, the finite-element models of whole-body human skeleton, and the multiparticle radiological dosimetry data of both the human and rat computational phantoms. The ontology of CPP was defined using MeSH and, with its all standardized models description implemented by M3L, a multiscale modeling language based on XML. Provided services based on Wiki concept include collaboration research, modeling version control, data sharing, online analysis of M3L documents. As a sample case, a multiscale model for human heart modeling, in which familiar hypertrophic cardiomyopathy was studied according to the structure-function relations from genetic level to organ level, is integrated into the framework and given for demonstration of the functionality of multiscale physiological modeling based on CPP.