The rice cropping practices, yields and pest injuries due to pathogens, insects and weeds were surveyed in 106 individual farmers’ fields within two experimental sites (Zhanyi and Xundian counties) in the main rice-producing area of Yunnan Province. The characterization of rice cropping patterns practices and multiple pest injury profiles and their relation with the rice yield were analyzed by using the nonparametric multivariate techniques: cluster analyses and correspondence analyses. The main results are: (1) six patterns of cropping practices (PR) are identified; PR1 and PR4 are common across sites while others are site-specific. PR1, PR2 and PR4 are related with high yield levels: PR1 corresponds to the highest agricultural input, PR2 to the higher input of mineral fertilizers, pesticides, water supply and labor. PR4 corresponds to the medium input level; (2) five pest injury profiles (IN) are determined; IN2 is common across sites. IN3 is the highest injury level of pest combinations and is related with the lowest yields in these profiles. IN1 correspond to the lowest injury level and is associated with the highest yields; (3) patterns of cropping practices and injury profiles are strongly associated at regional scale (χ², P < 0.0001). Both of them are good indicators to describe the variation in actual yields. The plot of correspondence analyses on the multi-dimension contingency table provides a framework that accurately reflects difference in cropping practices, pest injuries and yields between two sites, illustrates the diversity of patterns of cropping practices and injury profiles and indicates the potential for increased productivity in Xundian from the path of increasing yield levels (Y1-Y5). Results will provide some foundations for developing pest management strategies and improving rice production level at the regional scale.