The influence of water resources allocation patterns on root layers soil desalination and groundwater quality were investigated by monitoring different irrigation area from People’s Victory Canal irrigation district in Huang Huai Hai plain China that had been conducted well canal combined irrigation patterns from 1954. A typical area was chosen belong to the People’s Victory Canal irrigation district from 2013 to 2015. Precipitation of the area, surface water irrigation amount, groundwater consumption amount, salinity content in 0 to 100 cm soil layer and total dissolved solids in groundwater were monitored, the ratio of canal-well water (the ratio of surface water to groundwater irrigation amount, CWWR), soil salinity spatial dynamic, desalinization rate in 0 to 100 cm soil layer and sodium adsorption ratio (SAR) of groundwater were analyzed in the area. CWWR of 1st, 2nd, 3rd branch canals ranged from 0.72 to 1.03, 2.50 to 2.63, and 0.65 to 1.26 in 2013 to 2015, respectively. The soil salinity contents for the top 100 cm horizons in the 2nd branch canal irrigation area decreased slightly by 1.63% to 8.90% compared with the values in the 1st and 3rd branch canal irrigation districts while the water resources allocation patterns were conducted two years later. Compared with the area in the hydrological period in 2013, area of average soil salinity exceeded 0.32 mS/cm for the top 20 cm horizons has decreased notably in 2014 and 2015. Compared with the values in 2014, the average TDS concentration of groundwater increased by 18.66% in the study area in 2015, while the sodium adsorption ratio (SAR) values in the above-mentioned irrigation areas decreased by 23.58%, 36.82%, and 53.37% in the normal period in 2015. The combined well-canal irrigation pattern could represent a useful water allocation method mainly because of the temporal and spatial regulation of water resources and root layer soil desalination; however, possible increases of TDS in the groundwater may cause potential ecosystem degradation risks after long-term water allocation in semi-arid areas. Thus, water allocation should be emphasized to maintain a healthy groundwater environment and sustainable stable yields of grain in combined canal-well irrigation districts