As byproducts of the direct growth of III–V materials on the on-axis Si(001) substrates via molecular beam epitaxy (MBE), antiphase boundaries (APBs) degrade the performance of optoelectronic devices. In this study, to grow APB-free GaAs, we propose a straightforward yet robust approach to address this challenge. Based on atomic force microscopy and transmission electron microscopy analyses, we present evidence that in situ annealing of a Si(001) substrate in an arsenic-free chamber environment can effectively modify the surface step distribution. After the substrate is annealed at 1100 °C for 40 min, the surface steps transition from a random distribution to a well-ordered alignment along the ⟨110⟩ direction. This alignment meets the criteria for APB burial, thereby enabling the growth of APB-free layers on the substrate. A GaAs nucleation layer (NL) is subsequently deposited at a low temperature to establish a terrace-driven initial phase distribution. Under this regime, a GaAs epilayer is grown via the migration-enhanced epitaxy growth method in an As4 environment with a controlled V/III ratio, allowing one domain to overgrow the other, thereby achieving APB burial. Moreover, we employ a temperature-ramping growth technique during the transition from the NL to the high-temperature GaAs epilayer, resulting in a high-quality, APB-free GaAs epilayer on an on-axis Si(001) substrate. And based on the APB-free GaAs epilayer, QD lasers have been fabricated and demonstrated room-temperature operation. This approach provides a promising solution for the large-scale fabrication of high-quality III–V optoelectronic devices on complementary metal–oxide–semiconductor (CMOS)-compatible Si(001) substrates via MBE.