The field of mechanical manufacturing is becoming more and more demanding on machining accuracy. It is essential to monitor and compensate the deformation of structural parts of a heavy-duty machine tool. The deformation of the base of a heavy-duty machine tool is an important factor that affects machining accuracy. The base is statically indeterminate and complex in load. It is difficult to reconstruct deformation by traditional methods. A reconstruction algorithm for determining bending deformation of the base of a heavy-duty machine tool using inverse Finite Element Method (iFEM) is presented. The base is equivalent to a multi-span beam which is divided into beam elements with support points as nodes. The deflection polynomial order of each element is analysed. According to the boundary conditions, the deformation compatibility conditions and the strain data measured by Fiber Bragg Grating (FBG), the deflection polynomial coefficients of a beam element are determined. Using the coordinate transformation, the deflection equation of the base is obtained. Both numerical verification and experiment were carried out. The deflection obtained by the reconstruction algorithm using iFEM and the actual deflection measured by laser displacement sensors were compared. The accuracy of the reconstruction algorithm is verified.