A dense and uniform c-AlPO4 and SiC whisker co-modified mullite coating was successfully prepared on SiC-coated C/SiC composites with a thickness of about 70 μm by hydrothermal electrophoretic deposition. The thermal cycling performance of the coating samples was evaluated by thermally cycling between 1773 K and room temperature in a corundum tube furnace. Results show that the addition of SiC whisker (SiCw-mullite coating) significantly improved the thermal cycling resistance of single mullite outer layer on account of the toughening mechanism of SiC whiskers, such as whisker bridging and crack deflection. Then, the addition of c-AlPO4 (c-AlPO4-SiCw-mullite coating, termed ASM coating) further improved the thermal cycling resistance on account of the healing and bonding performances of c-AlPO4 at high temperature. After 40 thermal cycles, the weight loss of ASM coating on SiC-coated C/SiC composites was 4.5% compared to 5.24% for the SiCw-mullite coating. The retention rate of compressive strength of ASM coating on SiC-coated C/SiC matrix was 80.66% compared to 73.65% for the SiCw-mullite coating.