The spray atomization of an injector significantly influences the performance and working life span of a bipropellant thruster of a spacecraft. Deep space exploration requires the thruster to be able to operate reliably at a low temperature range from −40 °C to 0 °C, so the effect of low temperature conditions on the atomization characteristics of injector spray is motivated to be comprehensively investigated. To study the swirl atomization characteristics of MMH (methylhydrazine), which is more difficult to atomize than NTO (nitrogen tetroxide), numerical simulations were conducted, employing the methods of VOF (volume of fluid) and LES (large eddy simulation) under low temperature conditions. The physical model with a nozzle size of 0.5 mm and boundary conditions with a velocity inlet of 3.89 m/s both follow the actual operation of thrusters. The development of spray atomization at low temperatures was observed through parametric comparisons, such as spray velocity, liquid total surface area, droplet particle size distribution, spray cone angle and breakup distance. When the temperature decreased from 20 °C to −40 °C at the same condition of flowrate inlet, those atomization characteristics of MMH propellant vary following these rules: the spray ejection velocity of MMH is significantly reduced by 7.7%, and gas-liquid disturbance sequentially decreases; the liquid film development is more stable, with a negative influence on atomization quality, causing difficulties for primary and secondary breakup, so the total surface area of droplets also decreases by 6.4%; the spatial distribution characteristics, spray cone angle and breakup distance vary less than 5%. Therefore, the low temperature condition can directly lower the combustion efficiency of thrusters with obvious performance degradation, but there are no significant changes in the propellant mixing and liquid film cooling. It is concluded that the bipropellant thruster can reliably work at low temperatures around −40 °C for deep space probe operation.