Deep root system is a putative drought resistant characteristic in rice, but the physiological relationship to grain production remains obscure. The objective was to functionally dissect whether deep root system is important for rice yield in upland fields with intermittent drought. Six rice genotypes with different root systems were grown in the two treatments which changed rhizospheric environment. One was 'root layer restriction', which restricted the rooting depth by laying water permeable sheets at depth. The other was 'drought screening bed', which let the surface soil be dried-up more rapidly by inserting gravel layer between top-soil and sub-soil layers to interrupt the capillary rise. In 'root layer restriction', the genotypes with larger canopy size more reduced pre-dawn leaf water potential under soil water deficit during early reproductive stage, while the amount of deep roots contributed to maintenance of higher leaf water potential without the presence of root restriction layer. On the other hand, nitrogen uptake and biomass production of genotypes having deep root systems were outstanding in 'drought screening bed' under rainfed condition, where intermittent soil water deficit occurred at mid-season. Plant water relations during early reproductive stage and shoot biomass were likely to affect sink size and hence grain yield. As a consequence, genotypes with deep root system out-yielded other cultivars in 'drought screening bed', while genotypic variation in grain yield was not observed in 'root layer restriction'. Our results showed that deep root system is advantageous to improve grain yield in upland fields, especially if mid-season soil water deficit occurs, due to maintaining better plant water relations or shoot growth.