The decade‐old antibiotic, polymyxin B (PMB), is regarded as the last line defense against gram‐negative “superbug.” However, the serious nephrotoxicity and neurotoxicity strongly obstruct further application of this highly effective antibiotic. Herein, a charge switchable polyion nanocomplex exhibiting pH‐sensitive property is proposed to deliver PMB which is expected to improve the biosafety of PMB on the premise of retaining excellent antibacterial activity. The polyion nanocomplex is prepared through electrostatic interaction of positively charged PMB and negatively charged 2,3‐dimethyl maleic anhydride (DA) grafted chitoligosaccharide (CS). The negative charge of CS‐DA will convert to positive due to the hydrolysis of amide bonds in acidic infectious environment, leading to the disassembly of CS‐DA/PMB nanocomplex and release of PMB. CS‐DA/PMB nanocomplex does not show significant toxicity to mammalian cells while retaining excellent bactericidal capability equivalent to free PMB. The nephrotoxicity and neurotoxicity of CS‐DA/PMB dramatically decrease compared to free PMB. Moreover, CS‐DA/PMB nanocomplex exhibits superior bactericidal activity against Pseudomonas aeruginosa in an acute lung infection mouse model. The pH‐sensitive polyion nanocomplexes may provide a new way to reduce the side effects of highly toxic antibiotics without reducing their intrinsic antibacterial activity, which is the key factor to achieve extensive in vivo clinical applications.