A system and method for predicting an analytical abnormality are provided. The method for predicting an analytical abnormality may include generating a signal generation model and an analysis model for a design object based on first analysis data, applying a signal generated by the signal generation model to the analysis model based on second analysis data to calculate one or more estimated values, comparing the estimated values and the second analysis data to generate a plurality of early warning information, and determining whether to output an early warning based on whether the plurality of early warning information satisfy a preset condition.