Metal organic chemical vapor deposition (MOCVD) is a key means of epitaxy of heterojunction semiconductor material, the uniformity of its epitaxial layer thickness will directly affect the yield of the product, especially the vertical cavity surface emitting device, which has a higher requirement for thickness uniformity. For the multi-MO nozzle vertical reaction cavity MOCVD, this paper combines theory and experiment to give an effective method of improving the epitaxial layer thickness uniformity through adjusting the flow rate of each MO nozzle. Firstly, each MO source nozzle is equivalent to an evaporation surface source, and an equivalent height is introduced to cover the relevant epitaxial parameters of MOCVD and the quantitative relationship between the epitaxial layer thickness and the flow rate of each MO source nozzle is established by taking three MO source nozzles as an example. After that, the model parameters are extracted by fitting through the least squares method based on the experimentally measured epitaxial layer thickness distribution results. Finally, based on the extracted model parameters, a method to optimize the epitaxial layer thickness uniformity is given. Accordingly, the AlGaAs resonant cavity structure, which is easy to accurately test the epitaxial layer thickness, is designed and epitaxially grown by using the EMCORE D125 MOCVD system. The statistical results of the mapping reflection spectra of the 4-inch epitaxial wafers are that the average wavelength of the cavity mode is 651.89 nm, with a standard deviation of 1.03 nm, and thickness uniformity of 0.16% is achieved. At the same time, epitaxial growth of GaInP quantum well structure, 4-inch epitaxial wafers mapping photoluminescence spectrum statistics for the average peak wavelength of 653.3 nm, the standard deviation of only 0.46 nm, and peak wavelength uniformity of 0.07% are achieved. Both the wavelength uniformity of cavity mode and the peak wavelength uniformity of quantum well fully meet the requirements of vertical cavity surface emitting device. The method of adjusting epitaxial layer thickness uniformity proposed in this paper is simple, effective, and fast, and it can be further extended to vertical reaction cavity MOCVD systems with more than four MO nozzles.