In a method of controlling a manufacturing process, operating conditions of plural process steps are monitored during the manufacturing process. A degree of risk is calculated for each of a malfunction operating condition step and subsequent steps. The degree of risk is classified into plural levels and is determined in accordance with a risk point on the basis of the minimum WIP, actual WIP, target WIP, and a weighting factor. A priority of the manufacturing process needing recovery is determined in response to the degree of risk, and an operating condition of the manufacturing process is controlled in response to the priority determination.