The heterogeneity in biofilms is a major challenge in biofilm therapies due to different susceptibility of bacteria and extracellular polymeric substances (EPS) to antibacterial agents. Here, we describe a therapeutic strategy that overcame biofilm heterogeneity, where antibacterial agent (NO) and EPS dispersant (reactive oxygen species (ROS)‐inducing Fe3+) were separately loaded in the yolk and shell compartment of a yolk–shell nanoplatform. Compared with traditional combinational chemotherapies which suffer from inconsistent pharmacokinetics profiles, this strategy drew on the pharmacokinetic complementarity of ROS and NO, where ROS with a short diffusion distance and a high redox potential corrupted the EPS, facilitating NO, which has a long diffusion distance and a broad antimicrobial spectrum, to penetrate the biofilm and eliminate the resident bacteria. Additionally, the construction of a three‐dimensional spherical biofilm model is novel and clinically relevant. A therapeutic strategy to overcome biofilm heterogeneity is presented, in which antibacterial agent (NO) and extracellular polymeric substances (EPS) dispersant (reactive oxygen species (ROS)‐inducing Fe3+) are separately loaded in the yolk and shell compartment of a yolk–shell nanoplatform. The spatiotemporally ordered release manner and pharmacokinetic complementarity of ROS and NO improve the anti‐biofilm outcome synergistically.