The Vrn-D1b allele associated with facultative growth habit was recently found in the wheat cultivars mostly distributed in the Yellow and Huai River Valley Winter Wheat Zone (YHWZ) in China. The objective of the present study was to understand the effects of Vrn-D1b on agronomic traits. A population of F3:8 derived lines, having the same allelic variation at all known vernalization loci except Vrn-D1 and photoperiod loci, was developed, from which 50 lines with homozygous Vrn-D1b genotype and 50 lines with homozygous vrn-D1 genotype were evaluated in two environments. The results showed that the Vrn-D1b-carrying lines had significantly higher grain yield (0.3 t ha−1, P ≤ 0.01), more kernels per spike (1.2, P ≤ 0.01), greater thousand kernel weight (0.8 g, P ≤ 0.05), higher seedling height (2.5 cm, P ≤ 0.01) and plant height (2.0 cm, P ≤ 0.01), fewer sterile spikelet number per spike (−0.3, P ≤ 0.01), earlier in both heading (1.0 days, P ≤ 0.01) and anthesis (1.0 days, P ≤ 0.01), compared to the vrn-D1-carrying lines. Grain yield was positively correlated with seedling height (r = 0.47, P ≤ 0.01), plant height (r = 0.37, P ≤ 0.01) and kernel number per spike (r = 0.51, P ≤ 0.01), but negatively correlated with the heading date (r = −0.50, P ≤ 0.01) and anthesis date (r = −0.55, P ≤ 0.01). Path analysis and clustering analysis based on the principal component analysis showed that the yield advantage of Vrn-D1b lines over vrn-D1 lines was attributed primarily to the increased kernel number per spike. The findings indicate that the Vrn-D1b allele had a direct or indirect effect on grain yield.