Nontransparent flat parts with weak rigidity are widely used in precision physics experiments, aerospace, and other fields in which parallelism is required. However, existing methods cannot meet requirements due to the limitation of measurement size and accuracy. This paper proposes a new method for measuring parallelism of nontransparent flat parts with high accuracy and then builds a submicrometer-level parallelism measuring system. The 3D model of the whole part is reconstructed by thickness and flatness, which are measured respectively. Subsequently, parallelism is evaluated by the principle of minimum directional zone. The method is verified by an experiment with a thin copper substrate sized ⊘200mm×2.48mm on the parallelism measuring system. The experiment result shows that the part's parallelism is 7.41 µm, and the expanded uncertainty of parallelism measurement system is 0.34 µm, k=2.