Multidirected acyclic graph (DAG) workflow scheduling is a key problem in the heterogeneous distributed environment in the distributed computing field. A hierarchical heterogeneous multi-DAG workflow problem (HHMDP) was proposed based on the different signal processing workflows produced by different grouping and scanning modes and their hierarchical processing in specific functional signal processing modules in a multigroup scan ultrasonic phased array (UPA) system. A heterogeneous predecessor earliest finish time (HPEFT) algorithm with predecessor pointer adjustment was proposed based on the improved heterogeneous earliest finish time (HEFT) algorithm. The experimental results denote that HPEFT reduces the makespan, ratio of the idle time slot (RITS), and missed deadline rate (MDR) by 3.87–57.68%, 0–6.53%, and 13–58%, respectively, and increases relative relaxation with respect to the deadline (RLD) by 2.27–8.58%, improving the frame rate and resource utilization and reducing the probability of exceeding the real-time period. The multigroup UPA instrument architecture in multi-DAG signal processing flow was also provided. By simulating and verifying the scheduling algorithm, the architecture and the HPEFT algorithm is proved to coordinate the order of each group of signal processing tasks for improving the instrument performance.