Long-term prediction of regional groundwater and salt dynamics is important for the agricultural sustainability in Hetao Irrigation District, where the water resources supply and demand contradiction is prominent. The mulched drip irrigation with the well-canal conjunctive irrigation will be applied to save water and control soil salinity. In this study, the improved mass balance model SaltMod by a loosely coupled strategy was used to simulate the long-term groundwater and salt dynamics under current situation and future situation under well-canal conjunctive irrigation with mulched drip irrigation to evaluate the agrucultural sustainability. In the loosely coupled model, 2 SaltMod models were used to simulate the canal-and well- irrigated areas separately. An exchange flux was added in the aquifer mass balance equation to link the canal- and well-irrigated areas. The improved SaltMod could handle with multiple irrigation sources and different groundwater levels in the groundwater aquifer, which makes it possible to be used in the well-canal conjunctive irrigated areas. Then the model was calibrated and validated with 15 years' observation data of the Longsheng well-canal irrigated area in Hetao Irrigation District, Inner Mongolia, China. The data in years between 2002 and 2005 were used as the calibration period and 2006—2016 were used as the validation period. Root mean squared error (RMSE) and relative error (RE) were used to evaluate the results. The results showed that the improved model performed well for calculating the groundwater depth and soil salinity for both canal-and well- irrigated areas. Then the model was used to predict the water flow and soil salinity dynamics in the next 100 years under the current irrigation condition. The results showed that it could sustain a long-term stabilization under the present irrigation practice in the Longsheng well-canal irrigated area. Then the model was applied to simulate the water and salt dynamics with different senarios under the well-canal conjunctive irrigation and the mulched drip irrigation. With the satisfactory result of soil salinity in the canal-irrigated area, the well-irrigated area was the concern, especially the root zone in the well-irrigated area. Different autumn irrigation frequency schemes, irrigation quotas in the crop growing season, groundwater depth in the well irrigation area and groundwater mineralizations were considered to be the impact factors on the soil salinity in the root zone of the well irrigation area. The results showed that, the irrigation quota and groundwater depth had little effects on the variation trend of soil salinity in the root zone of well irrigation area. The autumn irrigation frequency scheme and groundwater mineralization played very important roles on the variation trend of soil salinity. When the autumn irrigation frequency (AIF) was once every two years and the groundwater mineralization increased to 2.0 g/L, the root zone soil salinity would still be less than 3.0 g/kg after 100 years. It would exceed 3.0 g/kg after 60 years when the groundwater mineralization increased to 2.5 g/L. Considering the groundwater mineralization of 90% well-canal irrigated area was less than 2.0 g/L, we recommended that when exploiting groundwater for irrigation in Hetao Irrigation District, it was necessary to apply the water from Yellow River for autumn irrigation to wash out the soil salt. The autumn irrigation frequency was once every two years and the autumn irrigation quota was 180 mm. [ABSTRACT FROM AUTHOR]