Grain yield is an important trait for hexaploid triticale cultivars. In this study, 300 hexaploid triticale cultivars were sequenced using simplified genome sequencing technology to develop high-quality SNP markers on a genome-wide scale based on durum wheat (AABB) and rye (RR) reference genomes, respectively. And grain yields per plant, 1000-grain weight, number of grains per ear, number of panicles per plant, grain length, grain width, ear length and plant height of these cultivars were investigated in two years, association analysis were carried out in combination with grain yield-related traits data and SNPs, and candidate genes were screened. 874,612 and 459,28 SLAF tags were obtained with durum and rye reference genome, respectively, 22,105,336 and 21,383,860 SNPs was developed with durum and rye reference genome, respectively. 300 triticale cultivars could be divided into 9 and 6 subgroups with durum and rye genome as the reference genome with population structure analysis. 253 associated SNPs with triticale grain yield-related traits distributed on chromosomes 1A, 1B, 2A, 2B, 3A, 3B, 4A, 4B, 5A, 5B, 6B, 7A, 7B, 1R, 2R, 3R, 4R, 5R, 6R and 7R and the contribution rate of phenotypic variation is between 0.07%-49.31%. 74 significant SNPs were detected in both two years and BLUE values. 91 candidate genes for grain-yield traits were obtained. Functions of most of the genes have not been studied.