Understanding the genetic diversity of various rice (Oryza sativa L.) cultivars cultivated over time in China is of great significance for the selection of parent materials for targeted rice breeding and the cultivation of new desirable varieties. In this study, 36 pairs of SSR markers were used to compare and analyze the genetic diversity of 1610 rice varieties bred in China from the 1980s to the 2010s. A total of 1568 allelic mutations were detected, with each locus varying having from 16 to 115, with an average of 44 per marker. The average gene diversity index and the polymorphism information content (PIC) of each locus were 0.8403 and 0.8243, respectively. The genetic diversity parameter values of japonica (Oryza sativa L. subsp. japonica Kato) rice varieties were higher than those of indica (Oryza sativa L. subsp. indica Kato) varieties. Over time, original unique alleles are lost, and new unique alleles are added. The total number of alleles, the number of unique alleles, and the number of varieties with unique alleles tend to increase over decades of breeding. In all ages, indica rice contained the largest number of unique alleles (19) in the 2000s, and japonica rice contained the largest number of unique alleles (11) in the 2010s. The trends of gene diversity index and PIC values increased first and then decreased. Gene diversity indices and PIC for indica rice reached their maximums (0.698 and 0.664 respectively) in the 1990s and japonica rice reached its highest values for these diversity metrics (0.791 and 0.766 respectively) in the 2000s. Analysis of molecular variance showed that genetic variation was primarily derived from differences of varieties that were bred during a given period. Most of the pair-wise Fst comparisons between different periods were at a statistically significant level. Cluster analysis shows distinctions in the genetic relationship of varieties bred in the twentieth century and the twenty-first century, but the genetic relationship between the varieties is relatively close when comparing within the twentieth or twenty-firs century, respectively. Our study will provide a scientific basis for the effective protection and efficient use of rice germplasm resources.