We report the crystal structure of allanite-(Ce), with composition (Ca1.0REE0.9□0.1)Σ2.0(Al1.46Fe3+0.52Fe2+0.76Mg0.12Ti0.15)Σ3.01Si3O12(OH) from the Xinfeng rare earth element (REE)-bearing granite in Guangdong Province, China. It has the unit cell a = 8.9550(4) Å, b = 5.77875(16) Å, c = 10.2053(4) Å, β = 114.929(5)° and Z = 2 in space group P21/m and is characterised by site splitting at M3 into M3a and M3b, at a distance of 0.38(3) Å, which are occupied partially by Fe0.764Mg0.12 and Ti0.15, respectively. The structure was determined by single-crystal X-ray diffraction and refined with anisotropic full-matrix least-squares refinement on F2 to R1 = 2.82%, wR2 = 7.77% for 1856 independent reflections (8772 collected reflections). However, M3 splitting is not present in either ferriallanite-(Ce) or epidote, in which M3 is almost fully occupied either by Fe2+ or by Fe3+. Comparisons of bond lengths and volumes in cation polyhedra among allanite-(Ce), ferriallanite-(Ce) and epidote tend to indicate that the essential factor that facilitates site splitting of M3 in allanite-(Ce) is heterovalent substitution and occupation of a crystallographic site between Fe2+(Mg2+/Mn2+)–Al3+(Ti4+), a common phenomenon in minerals, such as the plagioclase series. Fine structure analysis of the M3 split model revealed that deformation of A2 is related closely to distorted M3, which is consistent with Fe2+ incorporation following REE substitution.