Mass mortality of ark clam, Scapharca broughtonii, occurred in a local farm along the Bohai Sea, China in August 2017. Ostreid herpesvirus SB strain, which was the only pathogen previously reported in S. broughtonii, was not detected in moribund S. broughtonii. However, four kinds of bacteria were isolated from the hepatopancreas of naturally diseased S. broughtonii, and they were further identified based on 16S rDNA gene sequence analysis. These bacteria were closely related to Vibrio harveyi (A2-1), Microbulbifer variabilis (A2-2), V. alginolyticus (A2-3), and Pseudoalteromonas sp. (A2-4). Hemolysis test showed that A2-1 exhibited a strong hemolytic activity. The cumulative mortality of S. broughtonii with foot-injected A2-1 reached 100%, which was significantly higher than that of groups infected with other bacteria. Notably, temperature showed a significant effect on the mortality of S. broughtonii infected with A2-1, as the immersion challenged test showed 100% mortality occurred at 25 ± 2 °C on the 9th day, whereas no death was observed at 15 ± 2 °C on the 12th day. Temperature also significantly affected the growth rate and extracellular protein secretion of A2-1. In conclusion, this study is the first to report that V. harveyi is a pathogen that causes mass mortality in S. broughtonii, and the temperature is an important environmental factor that affects the virulence of A2–1 on S. broughtonii.