Abstract In this contribution, which is an extension of author’s research [1,2], an influence of the in two and three directions varying material properties on non-uniform torsion of the Functionally Graded Material (FGM) thin-walled beams is originally investigated. Based on the semi-analytical solution of the fourth order differential equation for non-uniform torsion, the local finite element equations of the twisted FGM beam are presented, considering the non-uniform torsion with effect of warping and secondary deformations due to the angle of twist. The warping part of the first derivative of the twist angle caused by the bimoment is considered as an additional degree of freedom at the beam nodes. The Multi-Layers Method (MLM) [3], and the Reference Beam Method (RBM) [4] are extended for homogenization of the spatially varying material properties and relevant stiffnesses in the real beam onto effective longitudinally varying ones in the homogenized beam for the load case of non-uniform torsion. The focus of the numerical investigation, with consideration of the warping and Deformation Effect due to the Secondary Torsional Moment (STMDE), is on elastostatic analysis of straight FGM beams with rectangular hollow cross-sections. The influence of the variation of the material properties with respect to two or three directions on the angle of twist and the bimoment normal and torsional shear stresses is investigated. The obtained results are compared with the ones calculated by a very fine mesh of standard solid finite elements. This FGM warping non-uniform torsion beam finite element can be used not only in torsional analysis of general thin-walled beams but also in the design of FGM sensors and actuators in mechatronics.