Further scale down the dimension of silicon-based integrated circuit is a crucial trend in semiconductor fabrication. One of the most critical issues in the nano-device fabrication is to confirm the atomic structure evolution of the ultrathin shallow junction. In this report, UV Raman spectroscopy, X-ray photoelectron spectroscopy (XPS), X-ray absorption near edge structure (XANES) and reflective second harmonic generation (RSHG) are utilized to monitor the pulse laser induced atomic structure evolution of ultralow-energy high-dose Boron implanted Si(110) at room and cold substrate temperature. A peak feature around 480 cm−1 resolved in UV Raman spectra indicates the formation of Si-B bond after the laser irradiation. The red shift of binding energy of Si element (~99 eV) in XPS and the evolution of absorption peak (~196.2 eV) in XANES reveal that the changes in the chemical states of ultra shallow junction strongly correlate to the activation process of Boron implantation, which is confirmed by RSHG measurement. The substrate temperature effect in the recrystallization of Boron implanted region is also realized by cross-section high-resolution TEM (HRTEM). The phenomena of Si-B bond formation and ultra-shallow junction recrystallization can be traced and applied to improve the reliability of Si ultra shallow junction in the future.