In hot polycrystalline materials, when a vertical flat grain boundary meets a horizontal surface the grain boundary forms a groove in the surface. Mathematically modelling features of such thermal grooving mechanism is therefore very important in characterizing polycrystalline materials composed of tiny grains intersecting an external free surface. With this aim in mind, we formulate and investigate a novel inverse problem of reconstructing the unknown time-dependent source term entering the fourth-order parabolic equation of thermal grooving by surface diffusion from a given integral observation. We formulate and prove in Theorems 2.3–2.7 that this linear inverse problem is well-posed. However, in practice, the ideal regularity of data under which the inverse source problem is stable is never satisfied due to the inherent non-smoothness of the measurement. Consequently, this leads to the inverse problem with raw data becoming ill-posed. In order to obtain accurate and stable solutions, we develop and compare two numerical methods, namely, a time-discrete method and an optimization method. We obtain error estimates and convergence rates for the time-discrete method. For the optimization method, an objective functional, which is proved to be Fréchet differentiable, is introduced and the conjugate gradient method (CGM), regularized by the discrepancy principle, is developed to compute the minimizer yielding the source term. The results of two numerical tests illustrate the performance of the two methods for both exact and noisy measured data.