WJS01A is a stable cytoplasmic male sterility (CMS) line originated from Brassica juncea (B. juncea) with complete pollen abortion that is rarely affected by environmental conditions. The present study identified WJS01A based on its morphological, cytological, genetical and molecular biological characteristics to reveal its mechanism of pollen abortion and provide a theoretical basis for its application in rapeseed breeding. The results are as follows: (1) the inflorescence structures of WJS01A are similar to those of normal B. juncea. However, its flower bud size, flower opening angles and petal size are slightly smaller than those of B. juncea. The anthers and filaments of WJS01A are shorter than those of normal B. juncea, thus its stamen heights are dramatically less than the stigma. Meanwhile, its anthers are albino without producing pollens; (2) Through testing the restorer and maintainer relationship of sterile line WNJ01A in Brassica napus (B. napus) derived from WJS01A, Polima (Pol), Ogura (Ogu) and Kosena (Kos) CMS types, the results showed that that of WNJ01A is significantly different from those of Pol, Ogu and Kos. Only Hui01 could restore the fertility of WNJ01A; (3) WJS01A is a nonpollen sactype sterile line, and its pollen abortions occurred from the anther primordial stage to the archesporial cell stage; (4) Multiplex PCR analysis of mitochondrial sterility genes showed that WJS01A and WNJ01A could be clearly distinguished from Pol, Ogu and Kos. But the current primers cannot distinguish WJS01A from normal B. juncea; (5) Restriction fragment length polymorphism (RFLP) analysis of the mitochondrial genome indicated that all of the eight probe/enzyme combinations could distinguish WJS01A from the other four sterile lines. It revealed that WJS01A is a CMS type significantly different from Pol, Ogu and Kos. Exploiting WJS01A will broaden the current genetic basis of heterosis utilization in B. napus. Furthermore, it will provide new germplasm to solve the current issue of cytoplasmic simplification in heterosis utilization in B. napus.