Precise water management is essential for the efficient development of irrigated agricultural crops in the Hetao Irrigation Area of Inner Mongolia. Given the severe water scarcity in the region and the significant use of intercropping as a cropping method, the development of rational irrigation scheduling is crucial. The objective of this work was to combine the ISAREG model with wheat–sunflower intercropping crops in order to enhance the effectiveness of irrigation scheduling in intercropping systems. This was achieved by changing and verifying crucial parameters for simulating irrigation patterns in intercropping. We conducted an assessment of nine irrigation schedules for a wheat–sunflower intercropping system in order to provide a range of irrigation scenarios that effectively fulfill the water requirements of the system. In light of this, we suggested implementing restrictions on the dates and volumes of irrigation based on the demand for agricultural irrigation. This approach aimed to establish irrigation schedules that are highly efficient and tailored to the specific crops in the area. As a result, we achieved a water use efficiency rate of 100%, saved 28.78% of water resources, optimized crop irrigation schedules, and enhanced crop economics by 6.7%. This study presents a novel and efficient method to optimize agricultural irrigation schedules, boost agricultural water use efficiency, and maximize crop yields in order to promote sustainable agricultural development.