In order to reconstruct the unsteady pollution source term of groundwater for its identification, the finite difference scheme was used to discretize the equations, terminal observed data were appended, and an improved conjugate gradient algorithm was used to reconstruct the pollution source term. The results show that, whether the pollution source term is a continuous function or a discontinuous and non-differentiable function, it can be reconstructed. In addition, with consideration of measurement errors, the proposed method can reconstruct the source term effectively, indicating that the improved conjugate gradient algorithm is effective in reconstructing the groundwater pollution source term.