In this study, we report a novel method based on swept-source optical coherence tomography that involves the reconstruction of the three-dimensional structure of the human subcutaneous microvasculature. A handheld optical coherence tomography system that has been developed in our laboratory is employed as the human skin microvascular scanner in the proposed method. Further, the differential standard deviation observed in the logarithmic-intensity blood flow images in case of multi-frame B-scan is calculated, and the in vivo cross-section and en-face images of human skin are obtained. The experimental results denote that the proposed algorithm can generate image information of hemorrhagic flow better when compared with the existing differential standard deviation algorithm based on logarithmic intensity. Furthermore, the blood flow details that cannot be seen in the processed results obtained from the original algorithm can be clearly observed from the reconstructed image obtained by the proposed algorithm, which is useful for ensuring the practical application of the optical coherence tomography system in medical diagnosis of diseases,such as cancer, diabetes, and wine stains.