The quantum confinement effect (QCE) of linear junctions of silicon icosahedral quantum dots (IQD) and pentagonal nanowires (PNW) was studied using DFT and semiempirical AM1 methods. The formation of complex IQD/PNW structures leads to the localization of the HOMO and LUMO on different parts of the system and to a pronounced blue shift of the band gap; the typical QCE with a monotonic decrease of the band gap upon the system size breaks down. A simple one-electron one-dimensional Schrodinger equation model is proposed for the description and explanation of the unconventional quantum confinement behavior of silicon IQD/PNW systems. On the basis of the theoretical models, the experimentally discovered deviations from the typical QCE for nanocrystalline silicon are explained.