Terahertz (THz) technology has been a great candidate for applications, including pharmaceutic analysis, chemical identification, and remote sensing and imaging due to its non-invasive and non-destructive properties. Among those applications, penetrating-type hyperspectral THz signals, which provide crucial material information, normally involve a noisy, complex mixture system. Additionally, the measured THz signals could be ill-conditioned due to the overlap of the material absorption peak in the measured bands. To address those issues, we consider penetrating-type signal mixtures and aim to develop a blind hyperspectral unmixing (HU) method without requiring any information from a prebuilt database. The proposed HYperspectral Penetrating-type Ellipsoidal ReconstructION (HYPERION) algorithm is unsupervised, not relying on collecting extensive data or sophisticated model training. Instead, it is developed based on elegant ellipsoidal geometry under a very mild requirement on data purity, whose excellent efficacy is experimentally demonstrated.