While it is generally accepted that triploid organisms are sterile, the exact reason of it remains elusive. With six copies of each homolog being segregated into four meiotic products, meiosis in triploid causes aneuploid gametes with reduced viability. However, it is unclear that if there are additional processes during meiosis also contribute to the sterility of triploid organisms. To examine the segregation behavior in details and find phenomena that have not been observed in previous studies of triploid, we constructed a pentaploid strain of Saccharomyces cerevisiae, so that each spore has at least one copy of each chromosome even if trivalent paring occurs and all three chromosomes segregate into one pole. Using single-nucleotide polymorphisms among strains, we generated genome-wide maps of crossover of all four products derived from eleven meioses. Among these 176 homolog pairing and segregation events, we observed 35 trivalent pairings and 10 bivalent/univalent pairings. The karyotype patterns indicated that following bivalent/univalent pairings, two combined homologs segregate to opposite poles while the third homolog randomly segregates to either pole, and following trivalent pairings, all three homologs randomly segregate to either pole rather than to the only one pole. In addition, high-resolution recombination maps revealed numerous chromosome breakage events, resulting in partial instead of the complete chromosomes in the meiotic products. Remarkably, the terminal region of all these fragments are long terminal repeat (LTR) sequence of genome, suggesting that chromosome breakage happens more easily in these regions. Taken together, we studied meiotic chromosome pairing and segregation patterns in pentaploidy, demonstrated the prevalence of multivalent paring during meiosis, and suggested the potential role of LTR in chromosome rearrangement that occurred frequently during the genomic evolution of yeast.