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The major factors associated with the manufactured structures and photon emission intensity distribution must be accurately identified for the complicated optical design parameters associated with micro-LED pixels. This study presents the methodologies and reveals the sequential calculating protocol in each layer for pixel-level optical simulations, based on which the boundary condition errors associated with common optical simulations can be corrected. Moreover, the optical effect on each epitaxial layer of the micro-LED design is revealed, and the rationality of the setting of the finite-radius receiver with a pseudo-extended substrate material is also explained with respect to the intrinsic and extrinsic pixel-intensity distribution properties. Finally, the design of experiments DOE L18 orthogonal array table is demonstrated by the Taguchi method to explore the principal factors for the parameter design of the micro-LED layers. The results indicate that the sapphire thickness, the P-GaN layer, the buffer layers, and an additional substrate plate are the four significant factors that primarily influence the luminous power and the corresponding uniformity on the exit pupil of micro-LEDs. Based on the luminous power uniformity, the signal-to-noise ratio in the sapphire thickness is 16.9, and the extended substrate plate is 9.8, which is ∼10 times > the interaction design parameter, such as the etching angle and reflective index of the extended substrate of the micro-LED pixel. These specific design factors can be the major optimization parameters for cost control and performance improvement.