According to the data of questionnaire survey on farmers’ cognition and participation willingness about the New Cooperative in some townships of Guangan and Dazhou Cities of Sichuan Province in the year 2008, farmers’ cognition about the New Rural Cooperative Medical System is analyzed by using the literatures, field investigation, semi-structured interviews, group discussion and other methods. At the same time, SPSS13.0 statistical software is used to carry out the Logistic Regression Analysis on the factors influencing the participation willingness of sample households. Result shows that although the New Rural Cooperative Medical System has been implemented throughout China for 6 years, there are only 57.75% households in underdeveloped western regions who know about the New Rural Cooperative Medical System quite well. Family income, expense, education degree, and comprehension degree of the New Rural Cooperative Medical System are the main factors affecting the farmers’ participation willingness. Based on this, countermeasures are put forward in order to promote the farmers to participate in the New Rural Cooperative Medical System.