To better understand the mechanism underlying nitrogen efficiency of rapeseed （Brassica napus L.） at seedling stage, two accessions with contrasting N efficiency （A294 with high efficiency, and A364 with low efficiency） were applied on investigating their C and N metabolism. The differences in root morphology, N absorption, transport and assimilation, and physiological indices related to photosynthetic C metabolism and gene expressions involved were compared between the two accessions through hydroponics, under normal N （CK, 9.5 mmol/L） and low N （LN, 0.475 mmol/L） nutrient solutions respectively. Results showed that, N-efficient accession A294 had stronger root system, with significantly higher plant biomass and N accumulation amount than those of A364 under low N condition. The ability for N absorption and transportation of A294 were also greater. However, activities of nitrate reductase and glutamine synthetase had no significant differences in two accessions. SPAD value, photosynthetic pigment content, net photosynthetic rate, and sucrose phosphate synthase gene （BnaSPS）expression of A294 leaves were all higher than those of A364. Further analysis found that, under low N stress, the expression of nitrate transporter BnaNPF7.3 in A294 root was remarkably higher than that of A364, while BnaNPF7.2b expression was significantly lower than A364. Root to leaf ratio of soluble sugar content in A294 was significantly lower, as well as root expression ofsucrose synthasegene （BnaSUS）thanA364. It is indicated that, N-efficient rapeseed accession A294 could distribute more nutrient elements （N） to seedling shoots under N deficiency stress, maintaining higher photosynthetic rate in leaves to guarantee a stronger metabolism of organisms; whereas, A364 could tend to allocate more nutrient elements （N） in root to promote growth and development. At the same time, the ratio of soluble sugar consumption in A364 roots was higher, which lead to higher root/shoot ratio in A364. Therefore, the distribution and consumption of N and energy substances （soluble sugar） of rapeseed respond to N deficiency stress could influence C metabolism of leaves （photosynthesis, sucrose synthesis）, then ultimately result in the N efficiency differences of rapeseed seedling.