Swept-source optical coherence tomography (SS-OCT) is gradually out-performing spectral-domain OCT (SD-OCT) in many aspects including sensitivity, speed, and ranging distance. However, its phase-stability is generally more difficult to achieve, compared to SD-OCT, which limited the functional imaging applications of phase-sensitive SSOCT. In this study, a novel phase stabilization technique is demonstrated with significant improvement in the phase stability of an SS-OCT system that is based on micro-electromechanical (MEMS) vertical cavity surface-emitting laser (VCSEL). Without any requirements of hardware modifications, this numerical phase stabilization technique features high tolerance to acquisition jitter, and significantly reduced budget in computational effort. We demonstrate that when measured with biological tissue, this technique enables a phase sensitivity of 89 mrad in highly scattering tissue, with image ranging distance of up to 12.5 mm at A-line scan rate of 100.3 kHz. We further compare the performances delivered by the phase-stabilization approach with conventional numerical approach for accuracy and computational efficiency. Imaging result of complex signal-based optical coherence tomography angiography (OCTA) and Doppler OCTA indicate that the proposed phase stabilization technique is robust, and efficient in improving the image contrast-to-noise ratio and extending OCTA depth range. The proposed technique can be universally applied to improve phase-stability in generic SS-OCT with different scale of scan rates without special hardware or extra imaging operations.