The invention provides a low-carbon low-volatility water-based flux and a preparation method thereof. The low-carbon low-volatility water-based flux is prepared from the following components, by mass:2-4.5% of an active agent, 1.5-4% of a surface active agent, 0-0.4% of a film-forming agent, 0.01-0.3% of an antioxidant, 0.01-0.4% of a corrosion inhibitor and the balance a solvent, specifically, the active agent is prepared by mixing at least two of succinic acid, benzoic acid, DL-malic acid and adipic acid at the mass ratio of greater than 0% respectively at the temperature of 30-60 DEG C; and the surface active agent is any one of AEC-9NA or TX-10 phosphate, or the surface active agent is prepared by mixing both of the AEC-9NA and TX-10 phosphate at the mass ratio of greater than 0% respectively. The flux has low solid residue content, no halogen, no rosin, low carbon, no volatile organic compound, no irritating odor, little corrosion to a circuit board, and round and bright solder joints. Besides, the flux is easy to manufacture, quite low in cost, convenient to store and transport, free of solder explosion, stable in chemical property, free of influence on physical health of operators and environmentally friendly.