The aqueous sodium-ion battery system is a safe and low-cost solution for large-scale energy storage, because of the abundance of sodium and inexpensive aqueous electrolytes. Although several positive electrode materials, for example, Na0.44MnO2, were proposed, few negative electrode materials, for example, activated carbon and NaTi2(PO4)3, are available. Here we show that Ti-substituted Na0.44MnO2 (Na0.44[Mn1-xTix]O2) with tunnel structure can be used as a negative electrode material for aqueous sodium-ion batteries. This material exhibits superior cyclability even without the special treatment of oxygen removal from the aqueous solution. Atomic-scale characterizations based on spherical aberration-corrected electron microscopy and ab initio calculations are utilized to accurately identify the Ti substitution sites and sodium storage mechanism. Ti substitution tunes the charge ordering property and reaction pathway, significantly smoothing the discharge/charge profiles and lowering the storage voltage. Both the fundamental understanding and practical demonstrations suggest that Na0.44[Mn1-xTix]O2 is a promising negative electrode material for aqueous sodium-ion batteries.