Single-crystal silicon (c-Si) is a vital component of photonic devices and has obvious advantages. Moreover, femtosecond-pulsed laser interactions with matter have been widely applied in micro/nanoscale processing. In this paper, we report the modification mechanisms of c-Si induced by a femtosecond laser (350 fs, 520 nm) at different pulse fluences, along with the mechanism of this technique to trim the phase error of c-Si-based devices. In this study, several distinct types of final micro/nanostructures, such as amorphization and ablation, were analyzed. The near-surface morphology was characterized using optical microscopy, scanning electron microscopy, and atomic force microscopy. The main physical modification processes were further analyzed using a two-temperature model. By employing Raman spectroscopy, we demonstrated that a higher laser fluence significantly contributes to the formation of more amorphous silicon components. The thickness of the amorphous layer was almost uniform (approximately 30 nm) at different induced fluences, as determined using transmission electron microscopy. From the ellipsometry measurements, we demonstrated that the refractive index increases for amorphization while the ablation decreases. In addition, we investigated the ability of the femtosecond laser to modify the effective index of c-Si microring waveguides by either amorphization or ablation. Both blue and red shifts of resonance spectra were achieved in the microring devices, resulting in double-direction trimming. Our results provide further insight into the femtosecond laser modification mechanism of c-Si and may be a practical method for dealing with the fabrication errors of c-Si-based photonic devices.