Aims Although comammox have been discovered in a variety of ecosystems, there are few studies in urban lakes. This paper attempted to confirm whether this ammonia‐oxidizing microbe exists in urban lakes and to determine the factors influencing its existence. Methods and Results This study investigated the diversity and abundance of comammox bacteria in sediments of a typical urban lake in China, and their ecological relationship with other ammonia‐oxidizing microorganisms. The phylogenetic analysis indicated that comammox clade A existed in the sediment of Lake Donghu, and the comammox bacteria co‐existed with ammonia‐oxidizing archaea (AOA), ammonia‐oxidizing bacteria (AOB) and anaerobic ammonia‐oxidizing (anammox) bacteria in the sediment of this lake. The abundances of the ammonia monooxygenase subunit A (amoA) genes for comammox, AOA, AOB, and anammox 16S rRNA were 2.43 × 10⁸, 1.07 × 10⁸, 3.24 × 10⁷, and 3.21 × 10¹¹ copies g^‐1 dry sediment, respectively. Moreover, the amoA gene abundance of comammox was positively correlated with that of AOA and AOB. The redundancy analysis (RDA) showed that the abundance of the comammox amoA gene was negatively correlated with the concentration of main indicators for nitrogen status in both the sediment and the water column, indicating that eutrophication may inhibit the growth of comammox bacteria. Conclusions Comammox bacteria play an important ecological role in the nitrogen cycle of urban lake sediments. Significance and Impact of the Study Our results indicated comammox bacteria were widespread in urban lakes and eutrophication may inhibit their growth.