Single-crystalline Si1−xGex thin films on Si (100) with low threading dislocation density (TDD) are highly desired for semiconductor industrials. It is challenging to suppress the TDD since there is a large mismatch (4.2%) between Ge and Si—it typically needs 106–107/cm2 TDD for strain relaxation, which could, however, cause device leakage under high voltage. Here, we grew Si1−xGex (x = 0.5–1) films on Si (001) by low temperature molecular beam epitaxy (LT-MBE) at 200 °C, which is much lower than the typical temperature of 450–600 °C. Encouragingly, the Si1−xGex thin films grown by LT-MBE have shown a dramatically reduced TDD down to the 103–104/cm2 level. Using transmission electron microscopy (TEM) with atomic resolution, we discovered a non-typical strain relaxation mechanism for epitaxial films grown by LT-MBE. There are multiple-layered structures being introduced along out-of-plane-direction during film growth, effectively relaxing the large strain through local shearing and subsequently leading to an order of magnitude lower TDD. We presented a model for the non-typical strain relaxation mechanism for Si1−xGex films grown on Si (001) by LT-MBE.