The need for an in vitro 3D scaffold that can substitute specific tissue-types is becoming increasingly prevalent in tissue engineering and stem cell research. As a promising candidate for engineered complex 3D tissue scaffolds, hydrogels have emerged as synthetic or natural polymers with tissue-like stiffness, biocompatibility and high permeability for oxygen, nutrients and other water-soluble metabolites, similar to the native extracellular matrix. However, high-resolution characterization of hydrogels and their three-dimensional porous structures still remains a challenge. In this research, hydroxypropyl cellulose methacrylate (HPC-MA) hydrogels were examined for the first time through X-ray ultramicroscopy (XuM), an imaging technique based on phase contrast and with high spatial resolution, to visualise, reconstruct and analyse 3D porous structures. This Scanning Electron Microscopy (SEM) based X-ray system produced projection images of 1.67 mm pixel size, with distinguishable hydrogel membrane structures. In addition, reconstruction of the tomographic series provides the complete geometry of individual pores and their spatial distribution and interconnectivity, which play vital roles in accurate prediction of the hydrogel's porous structure prior to and during its implantation in vivo. By further incorporating Atomic Force Microscopy (AFM), the elastic modulus of the hydrogel was determined and mechanical modelling of individual pores and the bulk scaffold also proved to be feasible. The commercialised platform we utilised offers prompt visualization and specialized simulation of customized 3D scaffolds for cell growth, which will be a unique application of tissue engineering in future personalized medicine.