B-containing 9Cr martensitic steels are attractive materials for specific industrial applications due to their excellent high-temperature strength and ductility. However, quenching large forgings with water or oil often results in cracking. The correlation between quenching crack and microstructure was established in this work to evaluate the selection of the quench cooling methods, which make it possible to mitigate the quench cracking by tailoring microstructural evolution. Kinetics dynamic analysis, microstructural characterization, and phase-field simulation were used to clarify the mechanism of mitigating quenching cracking. It is demonstrated that austempering produces a mixed microstructure consisting of lathy martensite, ultra-fine martensite, and a small amount of C-riched retained austensite. This mixed microstructure translates into refining the effective grain size and reducing the internal stress, reducing cracking propagation by reducing phase transformation stress and enhancing the coordinated deformation. Thus, the quenching cracking can be inhibition by tailoring the fraction of ultra-fine martensite and retained austensite in B-containing 9Cr steels.