The scallop (Pationopecten yessoenisis) is one of the most important aquaculture species in China. The main cultured areas are distributed in Chang-Shan archipelagos of Liaoning. But since 2007, the raft culture scallops P. yessoenisis disease outbreak has caused massive mortality in Changhai, Liaoning. The moribund scallops exhibited severe disease signs including brown deposit on the inner shell. So the cause of brown deposit symptom and the relationship with death of P. yessoenisis were analyzed. The epidemiological investigation and experiment of avoiding bite were used for researching the preliminary cause and formation of brown deposition syndrome. The infrared spectroscopy scanning was also used for studying the components of brown deposit. The result show that the cumulative mortality of P. yessoenisis cultured in aquaculture cage for avoiding bite was 87.60%, and the proportion of brown deposition syndrome was 74.50%. So biting or mechanical abrasion between scallops was not the cause of brown deposition syndrome; the FITR spectra of brown deposit was consistent with the FTIR of BSA, and had protein characteristic peaks of amide Ⅰ and amide Ⅲ, and the main component of brown deposit was protein; the brown deposition syndrome often happened in mid late June and early July when the temperature of seawater was 17 °C. 2017–2019, the proportion of brown deposition syndrome was 85.7%, 1.54% and 10.9% respectively, and the cumulative mortality of P. yessoenisis cultured in ordinary cage was 90.40%, 49.20% and 48.16%, and the proportion of brown deposition syndrome was significantly associated with the cumulative mortality of P. yessoenisis. So pathogenic infection may be the cause of brown deposition syndrome, and it had relationship with the massive mortality of P. yessoenisis.