In order to explain the water-saving effect of the alternative partial root-zone drip irrigation (APDI) and provide a theoretical basis and technical parameters for water-saving in protected culture cucumber cultivation, we studied the effects of APDI, fixed partial root-zone drip irrigation (FPDI) and conventional drip irrigation (CDI), on cucumber growth, physiological characteristics, yield, quality and water use efficiency (Jinyou No. 3). The trial was a completely randomized design with 65% of the soil field capacity set as irrigation lower limit, and 90% of field capacity set as irrigation higher limit. The results showed that: (1)With extension of the treatment time, stem diameter and leaf number did not show any significant difference, while the difference in leaf area and plant height of cucumber seedlings among the three irrigation patterns became more prominent. This proved that drought stress can significantly affect the relative leaf area expansion rate of greenhouse cucumber, because cell elongation is more sensitive to water stress than cell division. Under APDI treatment, cucumber root systems alternately subjected to water stress stimulated root growth, which promoted assimilation products in the root system, and then improved the root-shoot ratio, thus enhancing the water and nutrient uptake ability of the root system. (2) There was no significant difference in chlorophyll content in cucumber leaves between the APDI and CDI, but chlorophyll content decreased significantly under FPDI when compared with CDI. This was probably due to long-period drought stress in one side of its root system, resulting in greater suppression of root growth, the absorption ability of water and nutrients was decreased and the chlorophyll synthesis finally declined. Compared with CDI, the net photosynthetic rate of leaves declined slightly and the transpiration rate was significantly reduced under APDI, which resulted in a significant increase of leaf water use efficiency (WUE). Under FPDI treatment, the photosynthetic carbon assimilation rate decreased, meaning excessive excitation energy could not dissipate promptly, electron transport was then blocked, which resulted in a significant decrease of the actual photochemical efficiency and a significant increase of non-photochemical quenching. (3) Under the APDI pattern, there were no significant differences in soluble protein and soluble sugar content of the cucumber compared with CDI, but vitamin C content increased significantly; soluble sugar and soluble protein content of cucumber fruit were higher under FPDI than those of CDI and APDI, however, vitamin C content decreased significantly. (4) Compared with CDI, the irrigation quantity decreased by 28.3%and water use efficiency increased by 32% under FPDI, which indicated that FPDI can save a significant amount of water with only an 8%decreaseinyield. Compared with CDI, APDI decreased the yield by 1.5%, but reduced the irrigation amount by 17%, and increased water use efficiency by 18.6%, which means that the APDI pattern has a remarkable water-saving effect. Therefore, APDI can optimize the allocation of photosynthetic products, reducing growth redundancy and adjusting the allocation ratio between vegetative and reproductive growth. In conclusion, use of the APDI pattern can significantly improve the quality of cucumber fruit as well as increasing water use efficiency without a significant decrease in yield, so it can be applied in protected horticulture for water-saving irrigation, improving quality as well as irrigation efficiency, and has broad application prospects in arid and semi-arid regions.