As VLSI process node continue to shrink, chemical mechanical planarization (CMP) process for copper interconnect has become an essential technique for enabling many-layer interconnection. Recently, Edge-over-Erosion error (EoE-error), which originates from overpolishing and could cause yield loss, is observed in various CMP processes, while its mechanism is still unclear. To predict these errors, we propose an EoE-error prediction method that exploits machine learning algorithms. The proposed method consists of (1) error analysis stage, (2) layout parameter extraction stage, (3) model construction stage and (4) prediction stage. In the error analysis and parameter extraction stages, we analyze test chips and identify layout parameters which have an impact on EoE phenomenon. In the model construction stage, we construct a prediction model using the proposed multi-level machine learning method, and do predictions for designed layouts in the prediction stage. Experimental results show that the proposed method attained 2.7∼19.2% accuracy improvement of EoE-error prediction and 0.8∼10.1% improvement of non-EoE-error prediction compared with general machine learning methods. The proposed method makes it possible to prevent unexpected yield loss by recognizing EoE-errors before manufacturing.