Knowledge of radiation-induced helium bubble nucleation and growth in SiC is essential for applications in fusion and fission environments. Here we report the evolution of microstructure in nano-engineered (NE) 3C SiC, pre-implanted with helium, under heavy ion irradiation at 700 °C up to doses of 30 displacements per atom (dpa). Elastic recoil detection analysis confirms that the as-implanted helium depth profile does not change under irradiation to 30 dpa at 700 °C. While the helium bubble size distribution becomes narrower with increasing dose, the average size of bubbles remains unchanged and the density of bubbles increases somewhat with dose. These results are consistent with a long helium bubble incubation process under continued irradiation at 700 °C up to 30 dpa, similar to that reported under dual and triple beam irradiation at much higher temperatures. The formation of bubbles at this low temperature is enhanced by the nano-layered stacking fault structure in the NE SiC, which enhances point defect mobility parallel to the stacking faults. This stacking fault structure is stable at 700 °C up to 30 dpa and suppresses the formation of dislocation loops normally observed under these irradiation conditions.