Chlorophyll-a (Chl-a) concentration estimation by remote sensing is an important means for monitoring offshore water quality and eutrophication. In-situ hyperspectral data can achieve accurate analyses of Chl-a, but it is not suitable for regional inversion. Satellite remote sensing provides the possibility for regional inversion, but the precision is lower limited to atmospheric correction result. Therefore, this work uses machine learning to fuse in-situ hyperspectral data and Sentinel-2 multispectral instrument images to combine their complementary advantages, so as to improve the precision of regional Chl-a concentration inversion. First, the in-situ spectra were resampled based on the satellite spectral response function to obtain equivalent reflectance. Second, the spectral feature bands of Chl-a were determined by correlation analysis. Then three machine learning models, support vector regression, random forest, and back propagation neural network, were used to establish mapping relationships of feature bands between equivalent reflectance and satellite image reflectance so as to correct the satellite feature bands. Finally, Chl-a inversion models were constructed based on the satellite feature bands before and after correction. The results demonstrate that the corrected inversion model shows an increase in R2 by 0.25 and a decrease in mean relative error by 7.6%. This fusion method effectively improves the accuracy of large-scale Chl-a concentration estimation.