A quality prognostics system and a quality prognostics method for predicting the product quality during manufacturing processes are disclosed, wherein the current production tool parameters sensed during the manufacturing process and several previous quality data collected from the measurement tool are utilized to predict the future product quality, and a conjecture modeling step and prediction modeling step are performed respectively. The conjecture modeling step itself also can be applied for the purpose of virtual metrology. Further, a self-searching step and a self-adjusting step are performed for searching the best combination of various parameters/functions used by the conjecture algorithm or prediction algorithm; and meeting the requirements of new equipment parameters and conjecture/prediction accuracy.