This article studies the estimation of harmonic contribution (HC) and harmonic source current (HSC) for the system with multiple harmonic sources (SMHS). First, the limitation of voltage projection (VP) theory in the SMHS is analyzed. In this regard, this article proposes an indicator for quantifying HC based on the HSC. Then, this article clarifies the difference between measured harmonic emission current and unmeasurable HSC and proposes a harmonic current estimation algorithm based on the minimum mutual information (MMI) principle and the Bayesian optimization (BO). The effectiveness of the proposed indicator and algorithm is verified through simulation and experiment.