Chattering in composite deep-hole boring can directly affect surface processing quality and efficiency and has always been a research hotspot in machining mechanics. In this study, based on Euler–Bernoulli beam theory, the fine control equations for the cutting stability of composite variable-section boring bars were established using the Hamilton principle, in which the sectional change and internal damping of the material were considered. Next, using the Galerkin method and semi-discrete method, the effects of the taper ratio, damping ratio, length-to-diameter ratio, and ply angle on the free vibration characteristics and cutting stability were analyzed in detail. The results show that at a low damping ratio, both the first-order inherent frequency and boring stability can be enhanced with the increase in the taper ratio; at a large damping ratio, increasing the taper ratio can reduce the first-order inherent frequency and boring stability. Finally, the effects of the sectional change on the inherent frequency, displacement response, and convergence were analyzed. A numerical simulation was performed for the model reliability validation. The present research results can provide a theoretical basis and technical guidance for analyzing the cutting stability and fine control of composite variable-section boring bars with large length-to-diameter ratios.