Heterochromatin regions rich in tandem repeats have a high degree of chromatin condensation, which is not conducive to meiotic recombination, but some hot spots of chromosomal breakage, rearrangements and translocations are often located in the regions with tandem repeats. Therefore, it is necessary to understand the effect of tandem repeats on meiotic recombination. In this study, oligonucleotide probes derived from five tandem repeats (pSc119.2, pTa-535, pTa-275, pTa-713 and Oligo-18) were used to reveal the different structures of the long arms of 5A chromosome (5AL) in ten wheat cultivars, and the ten cultivars were used as parents to constructed four categories of F1 plants with different 5AL arms (5AL18/275 × 5AL713, 5AL535-18/275 × 5AL713, 5AL119-535-18/275 × 5AL18/275 and 5AL119-535-18 /275 × 5AL713). The F2 populations derived from the four kinds of F1 plants were used to explore the effect of chromosomal structure on meiotic recombination of 5A chromosomes. In the progeny derived from 5AL119-535-18/275 × 5AL18/275 and 5AL119-535-18/275 × 5AL18/275, a high level of chromosomal recombination was observed in the region between the tandem repeats of pSc119.2 and pTa535 on 5AL arm (L119-L535 interval). At the same time, breakage and non-homologous recombination of 5A chromosome were found in the progeny derived from the two hybrid combinations. Most of the breakpoints were located in or near the L119-L535 interval of 5AL arm, and the broken chromosomes were basically the 5A chromosomes with 5AL arms containing tandem repeats of pSc119.2, pTa535, pTa-713 and Oligo-18. These phenomena suggest that chromosomal regions with a high degree of aggregation of tandem repeats or heterochromatin influence both chromosomal recombination and the stability of chromosomal structure during meiosis. We speculate that the flanking regions of large tandem repeats are chromatin fragile sites prone to more DNA double-strand breaks (DSBs), thereby increasing the frequency of crossover recombination. However, regions with large differences in the composition of tandem repeats between homologous chromosomal segments may inhibit recombination, and will make part of the DSB repair blocked, thereby inducing chromosomal breakage and abnormal recombination.