Newly synthetic autotetraploid rice generally shows lower pollen fertility and seed setting rate in comparison to diploid rice, and this can hinder its own domestication and breeding. In this study, cytological analysis was used to demonstrate the imbalanced separation of homologous chromosomes occurred at meiosis I during the pollen mother cell development, and the early degeneration of tapetum cells in autotetraploid rice. We identified a total of 941 differentially expressed proteins (DEPs) in anthers, including 489 up-regulated and 452 down-regulated proteins. KOG analysis showed that the identified DEPs were related to post-translational modifications, such as protein ubiquitination. These modifications are related to chromatin remodeling and homologous recombination abnormalities during meiosis. The key proteins related to the pentose phosphate pathway (BGIOSGA016558, BGIOSGA022166, BGIOSGA028743) are significantly down-regulated, which can affect the failure of autotetraploid rice to provide the energy needed for cell development after polyploidization, and ultimately lead to the early degradation of the tapetum. Proteins (BGIOSGA017346and BGIOSGA027368) related to the degradation of glutenin are up-regulated, indicating that the decomposition of glutenin can lead to the early degradation of tapetum. These cytological and molecular evidences will help to promote our understanding of the differences in anther development between diploid and autotetraploid rice during meiosis.