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Different from the traditional size model, this paper is based on the phenomenological phonon confinement model. The phonon wave vector q, standard deviation σ and confinement coefficient β were comprehensively considered and their relative functional relationship was established. The discussions focused on the Raman shift and asymmetry broadening of the amorphous coated silicon nanocrystals brought by the size effect. The results showed that, for the silicon nanocrystals embedded in amorphous matrix, the confinement coefficient β involved the influence of the limitation barrier height to the Raman shift. As the size of the silicon nanocrystals decreased, the q changed from quasi-continuous form to discrete form participating the scattering and this discrete q can more accurately fit the Raman spectral lines of small-sized silicon nanocrystals. Standard deviation σ was further changed to precisely adjust the asymmetry of Raman peaks. Finally, the theoretical model established in this paper was compared with the experimental results and literature data of the research group, and found that the comprehensive consideration of the synergistic effect of the q, σ and β was conducive to evaluating the size effect, crystal morphology and relative proportion of amorphous coated silicon nanocrystals.