Borosilicate glass is an ideal material for microfluidic chip substrates due to its excellent light transmittance and stable chemical properties. However, it is also prone to brittle fracture during processing, making it a typical difficult-to-machine material. As an emerging processing technology, longitudinal torsional ultrasonic assistant milling (LTUVAM) can effectively reduce the surface damage of glass materials and improve the proportion of plastic removal of materials. The mechanism of LTUVAM of borosilicate glass was studied in this paper. Critical undeformed chip thickness (hc) is a key factor in achieving plastic material removal. At present, the influence of LTUVAM on the hc is not clear. Therefore, in this paper, the material-specific cutting energy model in the LTUVAM process was established to predict the hc. Firstly, the motion path of LTUVAM was analyzed, and the undeformed chip thickness model and the tool-workpiece separation rate model were established. Then, based on the above model, the material-specific cutting energy model was established according to the material removal principle. Finally, an LTUVAM orthogonal experiment was carried out to study the surface quality of the material. The experimental results showed that with the increase of ultrasonic power, the roughness and side damage area increased first and then decreased. With the increase of spindle speed, it showed that the roughness and side damage area decreased first and then increased. With the increase of feed per tooth, it showed that the roughness increased first and then decreased, and then increased, and the side damage area increased first and then decreased. Through the analysis of the experimental and model results, the increase of the separation rate between the tool and the workpiece contributes to the increase of the hc and the improvement of the processing quality.