We report for the first time a new methodology to determine molecular configurations of a large molecular complex in a dynamical process on a metal surface by combining time-resolved tunneling spectroscopy (I-t) and density functional theory calculation (DFT). Two examples, (t-Bu)4-ZnPc and FePc, representing molecular rotation and lateral diffusion on Au(111) surfaces, respectively, were applied to demonstrate our method. Through analysis of statistical occupation time for each configuration, the molecular configuration numbers and energy differences between different configurations of these molecular systems could be unambiguously determined. These experimental results are further compared with DFT calculation to determine corresponding molecular configurations. Importantly, through the spatial I-t mapping, valuable insights of molecular surface diffusion paths are obtained.