Chlorophyll fluorescence is an important indicator of the physiological state of phytoplankton in water bodies. The new generation of ocean color satellite remote sensors usually sets fluorescence bands to detect the phytoplankton fluorescence line height (FLH). Yet, the Geostationary Ocean Color Imager (GOCI) offers no FLH products so far, and the FLH results calculated using the fluorescence band (680 nm) and the two baseline bands (660 and 745 nm) have numerous negative values and are quite different from the FLH products of other satellite ocean color sensors. To address this problem, we established an FLH retrieval algorithm suitable for GOCI. We simulated the spectral datasets of different water types using the radiative transfer model HydroLight and established the band conversion relationship from 680 to 685 nm based on the simulated datasets. The remote sensing reflectance after band conversion was applied to the FLH product inversion, significantly reducing the number of negative FLH values and appreciably improving data availability for GOCI FLH products (from 14.78% to 66.73% on average). The new FLH product has a good correlation with the field-measured data (R2 = 0.73), and the relative error was 6.95%. Moreover, after band conversion, the FLH products retrieved by GOCI are in good agreement with the FLH products of MODIS, and fusion products can be further produced to improve the spatiotemporal resolution of the data. In addition, the radiative transfer simulation datasets also revealed that changes in solar zenith angle have little effect on FLH inversion. The hourly GOCI-derived FLH has good spatiotemporal continuity and can clearly reflect the diurnal variation of FLH. It can provide a stable FLH algorithm for further recovery of time-series GOCI FLH products and research on diurnal changes in FLH.