Maize is widely planted throughout the world and has the highest yield of all the cereal crops. The arid region of Northwest China has become the largest base for seed-maize production, but water shortage is the bottleneck for its long-term sustainability. Investigating the transpiration of seed-maize plants will offer valuable information for suitable planting and irrigation strategies in this arid area. In this study, stem flow was measured using a heat balance method under alternate furrow irrigation and double-row ridge planting. Meteorological factors, soil water content(θ), soil temperature(Ts) and leaf area(LA) were also monitored during 2012 and 2013. The diurnal stem flow and seasonal dynamics of maize plants in the zones of south side female parent(SFP), north side female parent(NFP) and male parent(MP) were investigated. The order of stem flow rate was: SFP>MP>NFP. The relationships between stem flow and influential factors during three growth stages at different time scales were analyzed. On an hourly scale, solar radiation(Rs) was the main driving factor of stem flow. The influence of air temperature(Ta) during the maturity stage was significantly higher than in other periods. On a daily scale, Rs was the main driving factor of stem flow during the heading stage. During the filling growth stage, the main driving factor of NFP and MP stem flow was RH and Ts, respectively. However, during the maturity stage, the environmental factors had no significant influence on seed-maize stem flow. For different seed-maize plants, the main influential factors were different in each of the three growing seasons. Therefore, we identified them to accurately model the FP and MP stem flow and applied precision irrigation under alternate partial root-zone furrow irrigation to analyze major factors affecting stem flow in different scales. The arid region of Northwest China has become the largest base for seed-maize production, but water shortage is the bottleneck for its long-term sustainability. Investigating the transpiration of seed-maize plants will offer valuable information for suitable planting and irrigation strategies in this arid area. In this study, stem flow was measured using a heat balance method under alternate furrow irrigation and double-row ridge planting. Meteorological factors, soil water content (θ), soil temperature (Ts) and leaf area (LA) also monitored during 2012 and 2013. The diurnal stem flow and seasonal dynamics of maize plants in the zones of south side female parent (SFP), north side female parent The order of stem flow rate was: SFP> MP> NFP. The relationships between stem flow and influential factors during three growth stages at different time scale (NFP) and male parent (MP) were investigated. On an hourly scale, solar radiation (Rs) was the main driving factor of stem flow. The influence of air temperature (Ta) during the maturity stage was significantly higher than in other periods. On a daily scale, Rs was the main driving factor of stem flow during the heading stage. During the filling growth stage, the main driving factor of NFP and MP stem flow was RH and Ts, respectively. However, during the maturity stage, the environmental factors had no significant influence on seed-maize stem flow. For different seed-maize plants, the main influential factors were different in each of the three growing seasons. Therefore, we identified them to accurately model the FP and MP stem flow and applied precision irrigation under alternate partial root- zone furrow irrigation to analyze major factors stem flow in different scales.