Photosynthetic pigment concentration has strong relationship with nitrogen (N) concentration which is an essential element of plant growth and plays an important role in estimating the net primary productivity (NPP) in terrestrial ecosystem research and precision agriculture (PA). In this study, hyperspectral reflectance and pigment concentration of the upper three leaves of rice crop (Oryza sativa L.) with five N fertilization rates were measured in the laboratory. The results showed that there was no significant difference between the leaf hyperspectral reflectance and pigment concentrations in the visible and near-infrared (NIR) spectral regions at each leaf position. But in the shortwave infrared (SWIR) region, the difference of each two of the three leaf positions was obviously significant at level 0.05. The integrated hyperspectral index MCARI/OSAVI[670,800] had been proved to be better linear related with leaf pigment concentrations at different leave position. The result demonstrated that MCARI/OSAVI[670,800] was a reliable and stable hyperspectral index for estimating pigment concentration at leaf level.