Stiffness–toughness balance is an important issue in rubber toughened polymer blends. In this work, a facile and effective route to simultaneously toughen and reinforce polylactide (PLA) by regulating the distribution of core–shell rubber (CSR) nanoparticles with carbon black (CB) is reported. The PLA/CSR/CB nanocomposites are prepared via direct melt‐blending PLA, CSR, and CB nanoparticles with different self‐aggregate capabilities. The FTIR and DFT calculation results reveal that the interactions between CB and CSR are stronger than those between CB and PLA. Thus, CB nanoparticles with high self‐aggregate capability (HCB) can drive CSR nanoparticles to join into the HCB network structures and form CSR‐HCB network structures in the PLA/CSR/HCB nanocomposites. However, for the CB nanoparticles with low self‐aggregate capability (LCB), uniform dispersion of both CSR nanoparticles and small‐sized CB clusters in the PLA/CSR/LCB nanocomposites is observed. Compared to the network structures, the uniform dispersion structure can endow PLA/CSR/CB nanocomposites with much better stiffness–toughness balance performances. Additionally, the distribution of CSR nanoparticles on the rheological properties of PLA/CSR/CB nanocomposites are studied. This work reveals significant correlations between distribution of CSR nanoparticles and properties of PLA nanocomposites, which is helpful to prepare high‐performance PLA materials.