As power density continues to rise in modern integrated circuits, efficient thermal management has become a critical challenge. Microchannel heat sinks offer a promising solution due to their compact structure and high heat dissipation capability. Among various substrate materials, silicon is considered an ideal candidate for constructing embedded microchannels due to its excellent material properties and superior compatibility with standard integrated circuit manufacturing processes. This study presents a novel approach for fabricating embedded microchannels on Si(001) substrates using molecular beam epitaxy and in-situ high-temperature annealing. A patterned silicon substrate with periodic ridge structures was first fabricated on a Si(001) wafer using electron-beam lithography, reactive ion etching, and inductively coupled plasma etching. Subsequently, a silicon homoepitaxial film was grown on this patterned substrate via molecular beam epitaxy, forming an array of isolated micro-nano pores. These pores were then transformed into enlarged, buried microchannels through in-situ high-temperature annealing. This approach combines the design flexibility of patterned substrates with the atomic-level precision of epitaxial growth, enabling controllable adjustment of microchannel dimensions, distribution, and burial depth. The dynamic process of pore coalescence into continuous microchannels was analyzed through systematic observation of the morphological evolution during annealing. Finite element analysis was employed to investigate the influence of channel geometric parameters on internal stress distribution and to identify the key factors affecting structural stability. Simulation results indicate that the channel width is the most critical parameter determining its mechanical stability. Guided by these simulation insights, microchannel structures with a width of up to 130 μm were successfully fabricated experimentally, validating the feasibility of this process for producing wide microchannels. This bonding-free method reduces the separation between the microchannels and overlying electronic devices to several hundred nanometers, offering a new pathway for the fabrication of integrated microchannel heat sinks.