The invention provides a method and system for estimating sea ice thickness distribution based on least squares adjustment, which processes satellite altimetry data and extracts related parameters, including latitude and longitude, elevation, average sea surface height, orbit number, pulse peak value and pulse Accumulated standard deviation; sea ice freeboard height extraction, including interglacial channel identification based on satellite echo signal-related characteristic parameters, to obtain sea ice freeboard height; sea ice thickness estimation, based on conversion from sea ice freeboard to sea ice thickness relationship, establish a function model in the grid unit, establish an observation equation, and use the least squares adjustment to solve the corresponding sea ice thickness results; perform resampling and filling to obtain the final sea ice thickness distribution map. The present invention gets rid of the traditional method of using empirical values, avoids the uncertainty brought by conditions such as snow thickness and snow density under the special geographical location and climatic conditions of the sea ice area, thereby improving the estimation of sea ice thickness. measured reliability.