Molecular structure in dip-coated films of linear poly(ethylene imine) (LPEI) on a germanium (Ge) substrate in dried and hydrated conditions have been analyzed by infrared multiple-angle incidence resolution spectrometry (IR MAIRS). The MAIRS-IP (in-plane) and -OP (out-of-plane) spectra of the dried film exhibited largely different patterns from each other, which indicated that LPEI molecules had an apparent molecular orientation with respect to the substrate surface. Although the film exhibited no peak in X-ray diffraction patterns, the low-crystallinity film has been found to have highly oriented molecular structure. Many key bands indicated that the molecules were involved in the double-stranded helix structure, which is specific to the anhydrate crystal of LPEI, with nearly perpendicular orientation. The Davydov splitting of the NH stretching vibration mode was readily captured by the IR MAIRS spectra, which also supported the helix standing model. When the film was stored in a humid condition, on the other hand, IR MAIRS spectra revealed that the helix was resolved to be straight chains, but the perpendicular orientation was kept unchanged. In addition, the MAIRS spectra also revealed molecular orientation of the water molecules of crystallization. The unique molecular arrangements are understandable by considering that the stabilization energy in the polymer monolayer directly attached on the substrate surface is minimized by the standing-molecule arrangements.