The invention provides a seed selection method of anti-club root tuber mustard cytoplasmic male sterile hybrid. The method comprises the following steps: 1) taking tuber mustard conventional variety as a female parent and taking cabbage anti-club root antigen as a male parent for hybridization to obtain an anti-club root improvement-type mustard tuber male parental line; and 2) taking a mustard tuber hau cytoplasmic male sterile line as the female parent and taking the anti-club root improvement-type mustard tuber male parental line for hybridization to obtain the anti-club root tuber mustard cytoplasmic male sterile hybrid; the mustard tuber hau cytoplasmic male sterile hybrid takes natural mustard-type rape cytoplasmic male sterile line 6-102A as the female parent, and the mustard tuber 6-170 is used as the male parent for hybridization. The anti-club root tuber mustard cytoplasmic male sterile hybrid has the characteristics of high purity and anti-club root disease, and overcomes the defects of anti-club root disease, successive cropping obstacle and variety degeneration existed in the current mustard tuber varieties.