The biological functions of differently expressed proteins between superior and inferior spikelet grains were investigated based on the isobaric tags for relative and absolute quantification to further clarify the mechanism of rice grain filling at the proteomic level, as well as the response of inferior spikelets to drought dress (-20 kPa or -40 kPa). Compared with superior spikelets, inferior ones had lower sink strength due to the lower sink activities (lower expressions of ADP-glucose pyrophosphorylase, granule-bound starch synthase, starch branching enzyme and pullulanase) and smaller sink sizes (lower abundances of structural proteins). The slower and later grain filling resulted from the weaker decomposition and conversion of photoassimilate and the slower cell division. Moderate drought stress (-20 kPa) promoted the grain filling of inferior spikelets through regulating the proteins associated with photoassimilate supply and conversion. These proteins may be important targets for rice breeding programs that raise the rice yield under drought condition. The findings offer new insights into rice grain-filling and provide theoretical evidences for better quality control and scientific improvement of super rice in practice.