Easy and effective usage of computational resources is crucial for scientific calculations, both from the perspectives of timeliness and economic efficiency. This work proposes a bi‐level optimization framework to optimize the computational sequences. Machine‐learning (ML) assisted static load‐balancing, and different dynamic load‐balancing algorithms can be integrated. Consequently, the computational and scheduling engine of the ParaEngine is developed to invoke optimized quantum chemical (QC) calculations. Illustrated benchmark calculations include high‐throughput drug suit, solvent model, P38 protein, and SARS‐CoV‐2 systems. The results show that the usage rate of given computational resources for high throughput and large‐scale fragmentation QC calculations can primarily profit, and faster accomplishing computational tasks can be expected when employing high‐performance computing (HPC) clusters. We present a procedure for easy and effective implementations of quantum chemical (QC) calculations benefited from machine‐learning assisted scheduling optimization and different load‐balancing algorithms. Employing this procedure, we showed that the high throughput and large‐scale fragmentation QC calculations can primarily profit, and faster accomplishing computational tasks can be expected when employing HPC clusters.