Irrigation plays an important role in agricultural production, especially in arid and semi-arid regions. However, the conflict between water supply and demand will become more serious with increasing population. This study was to evaluate the effects of limited irrigation on regional-scale water movement and salt accumulation processes in agricultural areas. Due to frequent vertical interactions between the saturated groundwater zone and the unsaturated soil water zone and significant lateral groundwater movement between different horizontal areas in arid and semi-arid agricultural areas with shallow groundwater level, a quasi-three-dimensional (quasi-3D) model was adopted, which coupled one-dimensional (1D) soil water and salt movement and 3D groundwater and salt movement. The Yonglian irrigation area was used as the typical study site. Nine limited irrigation scenarios based on different allocations of irrigation water and hydrological years were set and analyzed. The main results were as follows: (1) The net groundwater recharge is negative under most of limited irrigation conditions, causing the decline of groundwater level ranging from 0.028 m to 0.199 m within one year. (2) With the decrease of irrigation and precipitation in farmland during the crop growth period, the groundwater recharge, groundwater recharge concentration, leaching efficiency coefficient will decrease linearly, while soil salt storage index will increase linearly. (3) Salts may accumulate in the root zone for dry years or normal years with autumn irrigation water less than 100 mm per unit area. (4) Lateral groundwater fluxes and salts contained in lateral groundwater fluxes will reduce approximately 30% and 40% under limited irrigation conditions. (5) The root zone will suffer from a very severe threat of soil salinization in farmlands in the future when considering the average annual increase rate of soil salt in the root zone is 3.6% under limited irrigation conditions, and necessarily intervenes are needed. The results could support decision-making for water-saving and soil salinity prevention in arid agricultural districts.