Background This study is aimed at investigating the association of Fibrillin-1 ( FBN1 ) and transforming growth factor β (TGF-β) signaling-related gene polymorphisms with the susceptibility of Stanford type B aortic dissection (AD) and its clinical prognostic outcomes. Methods Five single-nucleotide polymorphism (SNPs) ( FBN1 rs 145233125, rs201170905, rs11070646, TGFB1 rs1800469, and TGFB2 rs900) were analyzed in patients with Stanford type B AD (164) and healthy controls (317). Gene–gene and gene–environment interactions were assessed by generalized multifactor dimensionality reduction. A 4-year follow-up was performed for all AD patients. Results G carriers of FBN1 rs201170905 and TGFB1 rs1800469 have an increased risk of Stanford type B AD. The interaction of FBN1 , TGFB1 , TGFB2 and environmental promoted to the increased risk of type B AD (cross-validation consistency = 10/10, P = 0.001). Dominant models of FBN1 rs145233125 TC + CC genotype (P = 0.028), FBN1 rs201170905 AG + GG ( P = 0.047) and TGFB1 rs1800469 AG + GG ( P = 0.052) were associated with an increased risk of death of Stanford type B AD. The recessive model of FBN1 rs145233125 CC genotype ( P < 0.001), FBN1 rs201170905 GG ( P < 0.001), TGFB1 rs1800469 AG + GG genotype ( P = 0.011) was associated with an increased risk of recurrence of chest pain in Stanford type B AD. Conclusions The interactions of gene–gene and gene–environment are related with the risk of Stanford type B AD. C carriers of rs145233125, G carriers of rs201170905 and G carriers of rs1800469 may be the poor clinical outcome indicators of mortality and recurrent chest pain in Stanford type B AD. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01213-z.