Plant height as the main plant architecture trait is closely related with lodging resistance and yield in flax. In order to analyze the genetic mechanism of plant height, in this study, several populations derived from the cross of P.I.250089×Heiya15 were constructed, followed by the genetic analysis using the method of mixed inheritance separation analysis of major gene plus polygene of plant quantitative traits. The quantitative trait (QTL) mapping of flax plant height was performed using RIL population together with BSA method based on the next-generation sequencing technology. The results showed that the plant height of flax was controlled by two pairs of major genes with additive-dominate-epistatic effects plus poly-genes with additive-dominate-epistatic effects. The heritability of the major genes in B1, B2 and F2 generations was 7.68%, 0.0% and 13.86%, and that of polygenes was 70.88%, 0.0% and 0.0% respectively. The inheritance of flax plant height is dominated by epistatic effect of two major genes, followed by additive effect and dominant effect. QTL mapping revealed two candidate gene loci which were on chromosome 14, 5770000 bp-6100000 bp and 6920000 bp-9400000 bp, with interval sizes of 0.33 Mb and 2.48 Mb, respectively, harboring 176 candidate genes. Collectively, our results provided insight for revealing the genetic mechanism of plant height in flax breeding.