The invention relates to an underwater photon transmission simulation method based on vertical chlorophyll concentration distribution, and the method comprises the steps: building an underwater quantum channel vertical transmission model, dividing a sea area according to different chlorophyll concentrations of a seawater surface layer, and carrying out the analysis to obtain a change condition of a deep seawater attenuation coefficient; and then using a Monte Carlo method to simulate the underwater transmission characteristic change trend of polarized photons, and realizing the uncertainty of the photon scattering process through random sampling. According to the simulation method, measurement of deep seawater parameters is avoided, and compared with a traditional method for describing seawater attenuation characteristics through a single parameter, the method is closer to reality, description of the seawater characteristics is more specific, practicability is high, and the method is universally applicable to multiple sea areas. Calculation is simple, physical images are visual, and the photon transmission characteristics obtained through analysis can provide theoretical reference for application of underwater communication, detection and positioning technologies and the like.