LED array microscopy is a novel computational imaging technique that can achieve two-dimensional (2D) phase imaging and three-dimensional (3D) refractive index imaging with both high resolution and a large field of view. Although its experimental setup is simple, the errors caused by LED array position and light source central wavelength obviously decrease the quality of reconstructed results. To solve this problem, comprehensive error parameters optimized by the phase smoothing criterion are put forward in this paper. The central wavelength error and 3D misalignment model with six freedom degree errors of LED array are considered as the comprehensive error parameters when the spatial positional and optical features of arbitrarily placed LED array are unknown. Phase smoothing criterion is also introduced to the cost function for optimizing comprehensive error parameters to improve the convergence results. Compared with current system correction methods, the simulation and experimental results show that the proposed method in this paper has the best reconstruction accuracy, which can be well applied to an LED array microscope system with unknown positional and optical features of the LED array. © 2023 Optica Publishing Group under the terms of the Optica Open Access Publishing Agreement.