Three-dimensional simulations of partially magnetized plasma are real challenges that actually limit the understanding of the discharge operations such as the role of kinetic instabilities using explicit Particle-In-Cell (PIC) schemes. The transition to high performance computing cannot overcome all the limits inherent to very high plasma densities and thin mesh sizes employed to avoid numerical heating. We have applied a recent method proposed in the literature [L. F. Ricketson and A. J. Cerfon, Plasma Phys. Controlled Fusion 59, 024002 (2017)] to model low temperature plasmas. This new approach, namely, the sparse grid combination technique, offers a gain in computational time by solving the problem on a reduced number of grid cells, hence allowing also the reduction of the total number of macroparticles in the system. We have modeled the example of the two-dimensional electron drift instability, which was extensively studied in the literature to explain the anomalous electron transport in a Hall thruster. Comparisons between standard and sparse grid PIC methods show an encouraging gain in the computational time with an acceptable level of error. This method offers a unique opportunity for future three-dimensional simulations of instabilities in partially magnetized low temperature plasmas.