Layer‐by‐layer alternating surface reconstructions of Si(001) 2×1 and 1×2 have been observed for the first time using reflection high‐energy electron diffraction (RHEED) during molecular beam epitaxy. RHEED intensity oscillations of the specular beam and two kinds of reconstruction related spots have been monitored simultaneously. It was found that stable alternating reconstructions can be observed on the surface with a single‐domain 2×1 structure obtained by high‐temperature annealing. One period of the RHEED intensity oscillation observed for the specular beam during the growth corresponds to a monatomic layer or a biatomic layer height depending not only on the electron beam incident azimuth but also the glancing angle.