Zirconolite-based structures have served as robust matrices for the incorporation of minor actinide-rich high-level waste (HLW). The co-doping effects are critical for exploring the phase evolution of zirconolite-based structures, thereby providing a guide for HLW immobilization. Nevertheless, few studies have studied the synergistic effect of high valent ion W6+ and Lanthanides (Ln, surrogates to minor actinides) co-doping. This study proposed a systematical study on the Ln-W (Ln = Nd, Sm, Gd, Ho, Yb) co-doping in zirconolite-derived structure using X-ray diffraction (XRD) and scanning electron microscope with energy dispersive X-ray spectroscopy (SEM-EDX). The results showed that near-single-phase zirconolite-2M was recorded for samples with low level doping of Ln-W (Nd–W, Sm–W and Gd–W with x = 0.05; Ho–W and Yb–W with x = 0.05–0.1), and its structure underwent a moderate expansion along the c-axis, as revealed by a Pawley refinement method. One key finding is that near-single-phase zirconolite-2M was recorded for samples with low level doping of Ln-W (Nd–W, Sm–W and Gd–W with x = 0.05; Ho–W and Yb–W with x = 0.05–0.1), and its structure underwent a moderate expansion along the c-axis, as revealed by a Pawley refinement method. Notably, in addition to a transformation from zirconolite-2M to pyrochlore, a pseudo-yellow phase CaWO4 was also noted with increasing co-doping contents. This work demonstrates that the high charge compensator W6+ and lanthanides can be simultaneously incorporated into zirconolite structure, and a different phase transformation was revealed compared to that in low valent element doping system, which gives a new insight into the optimization of HLW immobilization route.