Thinopyrum ponticum (2n = 10x = 70, EeEeEbEbEStEStStStStSt) is a member of the tertiary gene pool of wheat (Triticum aestivum L.), which has high tolerance to both biotic and abiotic stresses. In current study, twenty-one derivatives of common wheat and Th. ponticum were developed, including nine stable partial amphiploids, two alien disomic addition lines (5E, 5St) , six alien disomic substitution lines (1ESt (1D), 4ESt (4D), 6E (6D), 6St (6A), 7E (7B), 7ESt (7B)), and four double disomic substitution lines(1ESt (1D) + 6ESt (6D), 1ESt (1B) + 6ESt (6D), 2E (2D) + 4ESt (4B), 2E (2D) + 7E (7A)). These derivatives of Th. ponticum were served as an important supplementary source of useful genes for wheat improvement and breeding. Additionally, we developed ten new wheat varieties (Xinong 509, Xinong 511, Xinong 529, Xinong 733, Xinong 172, Xinong 519, Xinong 518, Xinong 533, Xinong 161, and Shaanmai 159) from Th. ponticum, which showed inordinately resistant to stripe rust, powdery mildew, and Fusarium head blight, as well as high qualities. Furthermore, we generated a total of 100 × coverage of Illumina and 30 × coverage of PacBio HiFi sequences for Th. ponticum, yielding a 36.93-Gbp assembly with contig N50 of 16.17 Mb. A high-throughput chromatin conformation capture (Hi-C) based physical map was used to assemble 70 pseudo-chromosomes that anchored 36.29 Gbp of the genome (98.28%). A total of 438 complete gene models among 458 (95.63%) conserved core eukaryotic genes (CEGs) in CEGMA and 1,580 (97.89%) among 1,440 conserved genes in BUSCO were recalled in our assembly. Genome re-sequencing of XN511 pedigree revealed that the genetic contribution of Th. ponticum to their derived cultivars varied from 0.95% to 1.21%. We expect that the derivatives and high-quality reference of Th. ponticum provide valuable resources for future basic research and wheat breeding.