Energy-efficient bioethanol production from plant biomass is in high demand, and one of the most promising procedures reported to date is one-pot ethanol production, that is, the production of ethanol from biomass in the same reaction pot, such as industrial first-generation bioethanol. This process requires cellulose solvents whose toxicity toward fermentative microorganisms is extremely low. Herein, we have developed a low-toxic zwitterionic cellulose solvent known as 4-(1-(2-(2-methoxyethoxy)ethyl)imidazol-3-io)butyrate (OE2imC3C). OE2imC3C is the only reported solvent that satisfies the following properties: being liquid at mild temperature and having good cellulose dissolution ability and low toxicity, even when including other types of solvents. We here investigated the relationship between the chemical structures and properties by synthesizing 22 zwitterions. Long alkyl- or oligoether chains attached to the cation (cation tails) were necessary to be a liquid. The zwitterions, except for that with an octyl tail, exhibited biocompatibility. Interestingly, the spacers of the zwitterions, alkyl chains between the cations and anions, were expected to be inert, but affected the toxicity. The molecular mechanisms were investigated using molecular dynamics simulations. The zwitterions exhibiting low toxicity scarcely inserted their cation tails into cell membrane and thus did not rupture the cell membrane. Ionic liquids, which have free cations and anions, induced molecular-level disruption of the cell membrane, suggesting that the zwitterion structure is a critical factor for low toxicity. The spacers, which were expected to be inert, shifted the solvent cluster structures in the bulk phase and induced molecular-level disruption of the cell membrane. The requirements for low-toxic cellulose solvents are zwitterionic structures, carboxylate anions, long polar cation tails, and in some cases, short spacers.