AbstractGrains at different positions on rice panicles differ greatly in weight and quality, but few studies have focused on the effect of dep1 that influences panicle morphology and grain number on grain weight and quality at different spikelet positions and under different backgrounds. To clarify this, we compared spikelet characteristics and grain quality in the superior spikelets (SS) and inferior spikelets (IS), as well as sink‐, source‐ and flow‐related traits between NIL‐dep1 (AKI‐dep1 and LG5‐dep1) and NIL‐DEP1 (AKI‐DEP1 and LG5‐DEP1) under the Akitakomachi (AKI) and Liaogeng5 (LG5) backgrounds. The grain weight and quality in SS did not significantly differ between NIL‐dep1 and NIL‐DEP1 under the two backgrounds. However, the effect of dep1 on grain weight and quality in IS varied with background. AKI‐dep1 significantly decreased the grain weight, processing quality, and eating and cooking quality in IS compared with AKI‐DEP1, possibly due to poor grain filling and the lack of an adequate source supply and vascular system to fully meet the increased sink size. With the exception of appearance quality, the grain weight and quality of IS of LG5‐dep1 were similar to LG5‐DEP1, mainly due to the enlarged vascular system and similar grain filling rate and source supply. We concluded that the varied effects of dep1 on grain weight and quality under the two backgrounds could be attributed to differences in grain filling and source−sink−flow relationships.