Nitrogen removal of petrochemical wastewater through partial nitritation/anammox (PN/A) is appealing, but its feasibility and stability under toxic inhibition remain unclear. This study started a PN/A granular sludge system in a membrane bioreactor and fed it with diluted acrylic fiber wastewater. During long-term operation, the nitritation and anammox performance remained stable at a 30% volume ratio, and declined with increasing volume ratio, resulting in deteriorated nitrogen removal. Meanwhile, the short-term inhibition batch tests further showed that ammonia oxidation bacteria (AOB) in the flocs were suppressed while anammox bacteria (AnAOB) in the granules were not affected. Further analysis indicated suppression of AnAOB over the long-term operation, which was mainly caused by the disintegration of granules as demonstrated by sludge morphology. This selective inhibition is associated with variational sludge morphology, and the distribution of functional bacteria plays an important role in the feasibility and stability of PN/A treating acrylic fiber wastewater. As above, this study demonstrated the feasibility of PN/A for acrylic fiber wastewater treatment, but wastewater dilution or pre-treatment is still required for efficient nitrogen removal.