Allopolyploid plants are hybrids that contain two copies of the genome from each parent. The study of the genome structure and gene expression pattern of newly synthesized allopolyploid provides novel opportunities to generate functional diversification between homoeologous genes and genomes. In this study, the intergeneric hybrids F1 and octoploid Triticale derived from the hybridization of common wheat cv. HuiXianHong (AABBDD, 2n = 42, Ta) and Secale cereale cv. JingZhou rye (RR, 2n = 14, Sc) were used for exploring genes expression patterns caused by hybridization and polyploidization in three tissues, flag leaf, spikelet, and stem. The expression levels dominance (ELD) both in hybrid F1 and Triticale also showing preference toward common wheat (Ta) in all tissues, but the orthologous genes class flipped over each other in diploidization. About 20% of the homologous gene expression bias to Ta in hybrid F1 became balanced in Triticale, while 20% of the genes that were originally expressed balance in F1 became bias to Ta in the Triticale. Genes of Ta were downregulated in Triticale mainly distributed on 2A, 4A, 2B, and 7D chromosomes, where the chromosome structure was detected by fluorescence in situ hybridization (FISH) study. Our study reveals the global gene expression patterns in the hybrid F1 and octoploid Triticale, and provided a good reference to study the consequences of polyploidy between wheat and its wild relatives.