The rice cropping practices, pest injuries (due to pathogens, insects, and weeds) and yields were surveyed in 106 individual farmers′ fields, in the main rice-producing area of Yunnan Province: Zhanyi and Xundian counties (two experimental sites). The characterization of patterns of rice cropping 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, whiles 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 and PR4 to the medium input from the view of mineral fertilizers, pesticides, water supply and labor input; (2) five pest injury profiles (IN) are determined; IN2 is common across sites, whiles others are site-specific; IN3 is the highest injury level of pest combinations in five profiles, related with the lowest yields in these profiles, whiles IN1 is the lowest injury level, 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 available for a good description of the variation in actual yield; the plot of correspondence analyses on 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.