In this article, a newly developed multiple-source meshless method (MSMM) capable of solving inverse heat conduction problems in two dimensions is presented. Evolved from the collocation Trefftz method (CTM), the MSMM approximates the solution by using many source points through the addition theorem such that the ill-posedness is greatly reduced. The MSMM has the same superiorities as the CTM, such as the boundary discretization only, and is advantageous for solving inverse problems. Several numerical examples are conducted to validate the accuracy of solving inverse heat conduction problems using boundary conditions with different levels of noise. Moreover, the domain decomposition method is adopted for problems in the doubly-connected domain. The results demonstrate that the proposed method may recover the unknown data with remarkably high accuracy, even though the over-specified boundary data are assigned a portion that is less than 1/10 of the overall domain boundary.