In the study, the spark plasma sintering (SPS) method was adopted to fabricate Si3N4 ceramics with Y2O3-MgO additives. Specimens with different grain dimensions, grain shapes, α/β phase ratios, densities were obtained by changing the heating rate and dwell time of SPS. The relationship between the microstructure and the thermal conductivity was studied. Results show that the heating rate and the dwell time have great influence on the microstructure and properties of Si3N4 ceramics. Both equiaxed and columnar β- Si3N4 grains are formed during sintering, but the thermal conductivity of Si3N4 ceramics is affected only by columnar grains. The thermal conductivity of the ceramics increases together with the formation and the growth of the β- Si3N4 columnar grains.