Background: Low temperature seriously depressed the uptake, translocation from root to shoot and metabolism of nitrate and ammonium in thermophilic plants such as cucumber, and the growth of plant was inhibited accordingly. However, there was no breakthrough in the effect of low temperature on nitrogen transport over the years. Results: By using the non-invasive micro-test technology the net NO3- and NH4+ fluxes rate in root hair zone and vascular bundles of main root, stem, petiole, midrib, lateral vein, and shoot tip of cucumber seedlings under normal temperature (NT) and low temperature (LT) treatment were tested, respectively. Under LT treatment, the net NO3- flux rate in root hair zone and vascular bundles of cucumber seedlings decreased, while the net NH4+ flux rate in vascular bundles of midribs, lateral veins and shoot tips increased. In accordance with this, the relative expression of CsNRT1.4a in petioles and midribs was down-regulated, while the expressions of CsAMT1.2a~1.2c in midribs were up-regulated. The results of 15N isotope tracing showed that compared with NT treatment, NO3--N and NH4+-N uptake of the seedlings under LT treatment decreased 78.1% and 58.8%, respectively, and the concentration and proportion of both NO3--N and NH4+-N distributed in the shoot decreased. Under LT treatment, the actual nitrate reductase activity (NRAact) in roots didn’t change significantly, while NRAact in stems and petioles of LT treatment increased by 113.2% and 96.2%, respectively.Conclusion: In summary, the higher net NH4+ flux rate in leaves and young tissues may be due to the higher NRact in stems and petioles, which could reduce more NO3- to NH4+ so as to reduce the energy consumption in nitrogen transportation under low temperature.