Incarvillea sinensis var. przewalskii has attracted great attention because of the anticancer value of its alkaloids and the potential use of the species for ecological restoration. However, the scarcity of high-quality seeds has significantly hindered the cultivation and efficient utilization of this species. Understanding how seeds respond to maternal environmental conditions is crucial for developing high-yield and top-notch seed accessions, but the available knowledge in this area is limited. Here, we determined the effect of shading treatments on seed development, seed quality, and yield. Compared to the control, shade significantly increased the seed germination rate and 1000-seed weight by 29.2% and 25.6%, respectively. Regardless of light conditions, the seed germination rate and 1000-seed weight decreased by 7.13% and 37.5%, respectively, as the fruit positioned from base to apical. The seed yield per plant was 27.9% higher under shade than under the control treatment. The structural equation model showed that shade promoted seed yield through increasing flowers per reproductive branch and seed numbers per capsule. These findings suggest that adjusting shading conditions and optimizing inflorescence development can lead to high-yield and high-quality seeds. Additionally, prioritizing the number of flowers per reproductive branch and seeds per capsule in breeding programs can further enhance the seed yield of I. sinensis var. przewalskii.