Zircon lite is a candidate host for immobilizing long-lived radionuclides. Zirconolite-based glass-ceramics in the CaO-SiO2-Al2O3-TiO2-ZrO2-Nd2O3-Na2O matrix are a potential waste form for immobilizing actinide radionuclides and can offer double barriers to immobilize radioactive elements. However, the X-ray diffraction patterns of the zirconolite derived from the glass matrix (glass ceramic, GC) are significantly different from those prepared by powder sintering (PS). In this Article, the crystal structures of Al-Nd codoped zirconolite grown via the glass matrix route and the powder sintering route are investigated in detail. Two samples of Al-Nd codoped zirconolite were prepared: one was grown from a CaO-SiO2-Al2O3-TiO2-ZrO2-Nd2O3-Na2O glass matrix, and the other was prepared with a Ca0.73Nd0.25ZrTi1.75Al0.25O7 composition by powder sintering. The samples were then characterized using powder X-ray diffraction (PXRD), scanning electron microscopy (SEM), transmission electron microscopy-energy dispersive X-ray spectroscopy (TEM-EDX), and selected area electron diffraction (SAED). The chemical composition of the 100-500 nm zirconolite crystals grown from a glass matrix was determined by TEM-EDX to be Ca0.83Nd0.25Zr0.85Ti1.95Al0.11O7. PXRD and SAED results showed that these two Al-Nd codoped zirconolite phases were crystallized in space group C12/c1. The HRTEM images and SAED results showed that there were heavy stacking faults in the zirconolite crystals grown from the glass matrix. In contrast, far fewer defects were found in the zirconolite crystals prepared by powder sintering. The split-atom model was adopted for the first time to construct the Al-Nd codoped zirconolite structure grown from glass during the Rietveld refinement. The isostructural method assisted by Rietveld refinement was used to resolve the Al-Nd codoped zirconolite structures prepared by different methods. The occupancies of the cation sites were identified, and the distribution behavior of Nd3+ was further investigated. The results indicate that the heavy stacking faults may lead to substantial differences in the Al-Nd codoped zirconolite structures prepared by these two fabrication routes.