To gain a thorough understanding of the biological characteristics and genetic diversity of weedy rice in Jiangsu Reclamation Area and to tap into its potential high-quality genetic resources, this study conducted field planting, observation, and recording of 27 weedy rice samples collected from 19 agricultural areas within the Jiangsu Agricultural Reclamation System. Through principal component analysis and cluster analysis, we conducted a detailed analysis of the genetic diversity of these weedy rice materials. The results indicated that the weedy rice population in Jiangsu Reclamation Area exhibited certain advantages over cultivated rice in terms of length-to-width ratio, panicle length, number of grains per panicle, number of filled grains, and tillering ability. However, its seed setting rate is slightly lower than that of cultivated rice, and its thousand-grain weight is significantly lower. The peak tiller number, shattering rate, number of filled grains, total grain number, thousand-grain weight, and plant height in the weedy rice population exhibited considerable genetic variability and rich genetic diversity. Cluster analysis based on phenotypic traits and gene sequences obtained consistent results, roughly dividing the weedy rice population into five categories, with the FXW category tending towards japonica type, while the other categories tended towards indica type. This study provides a scientific basis for the effective management and utilization of weedy rice in Jiangsu Reclamation Area.