With standardization, informatization, scientificness, and rationalization are more and more popular in the research project management, the risk management becomes more and more important. In risk management, risks in research project should be ordered by their importance, and the influence of risks on project schedule and cost should be also analyzed. A Monte Carlo Simulation (MCS)-based method for quantifying the risk in research project is developed in order to analyze the importance, schedule as well as the cost of the project. Firstly, the method for risk data capturing and processing is developed on basis of the triangle distribution. Secondly, the circle and cost models are developed separately on basis of Earliest Start Time (EST), Earliest Finish Time (EFT) as well as the Cost Breakdown Structure (CBS). Thirdly, the sampling algorithm and flow based on MCS is defined, the analysis method for probabilistic risk error is also proposed. Finally, a leveled risk analysis method is also developed on basis of the risk quantification; the total risk is divided into the risk of project and risks of subprojects. A method for computing completion probability of appointive deadline constraint-oriented project is discussed; in the meantime, the method for analyzing subproject progress-oriented risks is developed by using the index of key targets which are Key Probability (KP) and Key Importance (KI).