The influence of the hierarchical nanometer-sized precipitates (NPs) on the microstructure evolution and mechanical properties of ultra-low carbon medium manganese quenching-partitioning-tempering (QPT) steel was studied. A unique combination of hierarchical NPs including lenticular Cu/Ni precipitates (>5 nm) and spherical (<1.5 nm) NiAl/Cu co-precipitates was obtained during QPT treatment. The shear mechanisms of spherical NPs mainly contribute to a strength enhancement of approximately 500–700 MPa, whereas the lenticular Cu/Ni precipitates result in an enhanced driving force for an abnormal austenite growth owing to the localized element enrichment and the interfacial incoherency, thereby obtaining a bimodal-grained distribution of austenite which possesses a wide mechanical stability. Thus, a continuous transformation-induced plasticity (TRIP) effect over the entire strain regime occurs, contributing to a good strain hardening capacity and superior ductility enhancement (uniform elongation change from 8% to 16%). However, the introduction of the hierarchical NPs not only inevitably creates a strong concentration of stress within the weak grain boundaries, but also leads to a detrimental transformation product from the blocky austenite with a low mechanical stability, thus resulting in the formation of intergranular cracks and a low impact toughness (20 J).