We are concerned with the nonlinear stability of the composite wave consisting of two planar viscous shock waves to the three-dimensional compressible Navier–Stokes system. It is shown that if the shock strengths are suitably small but not necessarily of the same order of magnitude, and the initial perturbations are suitably small without the zero-mass conditions, then there exists a unique, globally strong solution in time to the compressible Navier–Stokes system, which asymptotically approaches the corresponding composite wave up to time-dependent shifts in L^{\infty} norm. The proof employs the weighted relative entropy method, an L^{2} -contraction technique with time-dependent shifts to the shocks developed by Kang and Vasseur [J. Eur. Math. Soc. (JEMS) 23 (2021), 585–638; Invent. Math. 224 (2021), 55–146]. We perform the stability analysis within the original H^{2} -perturbation framework instead of using the anti-derivative technique. Compared with the previous work of the author and Wang [J. Eur. Math. Soc. (JEMS) (2023), DOI 10.4171/JEMS/1486] for the single shock case, a major difficulty is the construction of shifts to ensure that the two shock waves are well separated.