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Phytoplankton is a vital component of marine organisms, it plays a crucial role in material circulation, energy flow and information transmission. The study of phytoplankton communities is important to understand the carbon cycling and biodiversity, and the study on the biomass for a certain phytoplankton group can help understand the structural changes of phytoplankton communities. Diatoms are the dominant taxonomic group with the most abundant concentration in coastal water, and it provides solid photosynthetic capacity (about 40% of marine primary productivity). Meanwhile, diatoms concentration will indirectly affect the breeding progress of holoplankton. In this study, observation samples (n = 252) were collected in the marginal seas of the northwest Pacific Ocean, covering Bohai Sea (BS), Yellow Sea (YS), and East China Sea (ECS), from six cruise surveys that covered different seasons. The concentration of diatoms was calculated by phytoplankton pigments concentrations collected with high performance liquid chromatography method (HPLC), with CHEMTAX method, and the spatial distribution for measured diatoms concentration was analyzed. Based on in situ data parameters collected by multiple cruises, including phytoplankton absorption coefficients and diatoms concentration, we optimized Gaussian central bands and half-wave widths with derivative spectrum analysis and the peaks of the specific absorption spectrum, which were mentioned in existing research. Then the correlation coefficients between diatoms concentration and different Gaussian peaks, which decomposed by Gaussian function, were analyzed. We established the Gaussian peaks, which had the higher correlation coefficients with diatoms concentration, to establish the inversion model of diatoms concentration. The inversion models between Gaussian peaks and diatoms concentration were studied with different mathematical functions (linear function, quadratic function, logarithmic function, exponential function and power function), and the accuracy for each model was evaluated by two precision indicators (determination coefficients, R2 and median percent error, ME), so as to propose the optimal inversion model form. The parameters (A、B) were confirmed by leave one out methods later. The result of the research shows that: 1) The spatial distribution of measured diatoms concentration presented the characteristics that higher for nearshore and lower for offshore. The higher areas for BS appeared in the neighborhood, and the trend to central area was decreasing progressively. Similar to BS, the spatial distribution of measured diatoms concentration was higher for nearshore (Yangtze Estuary) and lower for offshore (central area) in both YS and ECS; 2) The evaluation indicators for our diatoms concentration inversion model are relatively high. Comparing the diatoms concentration modeled in this study and calculated by CHEMTAX method, and using leave one out methods to verify the accuracy between them, the determination coefficients (R2) is 0.79, the median error (ME) is 49%, and the p-value under 0.001. It should be noted that some deviation appears in the lower concentration (< 0.02 mg m-3); that’s why the range of application should be concluded in latter applications. In a word, the relatively high accuracy shows the applicability for the inversion model of diatoms concentration in this study, and the model lay the foundation for conducting the research for satellite remote sensing inversion of diatoms concentration.