This paper investigates the inverse problem of determining the time-dependent heat source and the temperature for the heat equation with a non-classical boundary and an integral over-determination conditions. The existence, uniqueness and continuous dependence upon the data of the classical solution of the inverse problem is shown by using the generalised Fourier method. Furthermore in the numerical process, the boundary element method (BEM) together with the second-order Tikhonov regularization is employed with the choice of regularization parameter based on the generalised cross-validation (GCV) criterion. Numerical results are presented and discussed.