Liquid scintillators are commonly used to detect low energy neutrinos from the reactors, sun, and earth. It is a challenge to reconstruct deposited energies for a large liquid scintillator detector. For detectors with multiple optical mediums such as JUNO and SNO+, the prediction of the propagation of detected photons is extremely difficult due to mixed optical processes such as Rayleigh scattering, refraction and total reflection at their boundaries. Calibration based reconstruction methods consume impractical time since a large number of calibration points are required in a giant detector. In this paper, we propose a new model-independent method to reconstruct deposited energies with minimum requirements on the calibration system. This method is validated with JUNO's offline software. Monte Carlo studies show that the energy non-uniformity can be controlled below 1%, which is crucial for JUNO to achieve 3% energy resolution.