The charge-per-mass of sand grains in natural windblown sand fluxes is important for understanding its contribution to atmospheric electric field and its effect on dust transport in atmosphere and the evolution of windblown sand fluxes. In many existing studies, the charge-per-mass of sand grains were usually averaged values, namely, the total charges divided by total mass of sand sample collected in a sand grain trap. In this paper, by conducting a field site experiment in Tengger Desert in western China, the charge-per-mass of individual grains of natural near-surface windblown sand fluxes are measured for the first time. A method is established for this purpose, which includes a well-designed silicone oil box used to trap sand grains and the grain trajectory imaging system for the retrieval of sand grains’ charges and sizes. The charge-per-mass of more than 900 grains are measured individually with good accuracy, from which the probability distributions of both charge-per-mass and grain size are obtained. The probability distribution of charge-per-mass of individual sand grains may provide more accurate estimations of charge distribution in natural windblown sand fluxes. On the other hand, these results of charge-per-mass are helpful for the validation of existing theories of charging mechanism of windblown sand fluxes.