A practical strategy for three-dimensional morphology measurement in the particle deposition process is of great importance to deepen the understanding of deposition physical processes. Due to the methodology limitations, it is difficult to obtain the formation process of deposition morphology. In this work, an in situ multi-perspective scanning (MPS) method using structured light was developed to capture the formation process of deposits. The point cloud registration algorithm was adopted to reconstruct the deposition morphology. Based on the validation results of Vernier caliper, the MPS method provides an uncertainty of ±0.056 mm at 4 mm. To verify the potential application of in situ measurement in gas turbine diagnostics, MPS method was preliminarily applied to the flat plate test with film cooling in particle-laden flow. The application demonstrated that this method successfully reconstructed the deposition morphology on a flat plate in the presence of film cooling. Furthermore, the obtained morphology results revealed that deposition roughness lied in the 0.35–0.56 mm and increased with an increase of blowing ratio. Additional comparisons with film cooling effectiveness showed the deposition distribution was related to the film cooling process. The detailed three-dimensional (3D) deposition morphology determined the mean curvature and mass of deposits, which may improve the prediction accuracy of deposition models in numerical simulations.