The effects of short-term waterlogging on physiological responses, fatty acid compositions and yield components of rapeseed at both the vegetative growth and the reproductive growth stages were assessed in this study. Waterlogged plants were treated for a period of 10 days at the vegetative growth stage and 4 days at the reproductive growth stage. The results show that photosynthesis and stomatal conductance at both the vegetative growth and the reproductive growth stage were significantly reduced during the waterlogging period and after the recovery period. When the plants were removed from water, photosynthesis and stomatal conductance progressively restored similar values to those of control plants within $2{sim}3$ days. Fatty acid compositions were unaffected by waterlogging treatment. However, yield components (pod number and pod length) of the waterlogged treated plants at the reproductive growth stage were significantly reduced. These results suggest that short-term waterlogging may thus influence oilseed yield component.