Sea surface chlorophyll data are the 8–day composite of MODIS–terra chlorophyll products from 2001 to 2019. The L3 data with a 4 km spatial resolution were extracted from 42°N-44.5°N and 65.5°W-71°W and interpolated spatially onto a 0.025°*0.025° grid. Cloud–free chlorophyll data were reconstructed using the Data INterpolation Empirical Orthogonal Function (DINEOF) method, which has been applied to fill the spatial gaps of satellite products without lowering their qualities. The original 8–day composite of MODIS–terra chlorophyll products are available at https://oceancolor.gsfc.nasa.gov. Only those spatial points without data due to clouds or sun glint are constructed using the DINEOF. chl_GOM_origin_and_DINEOF.mat is the surface chlorophyll data. lon_GOM_2D.mat and lat_GOM_2D.mat are longitude and latitude information. The data can be loaded directly using MATLAB (.mat file).