Abstract: Based on the survey data collected from 200 sampling stations by 14 cruises in Daya Bay of the South China Sea in 1988, 2004, 2008 and 2015, we analyzed the characteristics of the secondary productivity and P/B (secondary production/biomass) ratio of macrobenthos for nearly 30 years using Brey's empirical formula. The results show that: 1) Based on ash free dry mass (AFDM), the microbenthic secondary productivity and P/B ratio were 7.44 g·(m²·a)^–1 and 0.76 a^–1 in 1988, 11.34 g·(m²·a)^–1 and 0.86 a^–1 in 2004, 4.91 g·(m²·a)^–1 and 0.79 a^–1 in 2008, 2.93 g·(m²·a)^–1 and 0.47 a^–1 in 2015, respectively. The secondary productivity and the P/B ratio of macrobenthos increased during 1988−2004, then decreased during 2004−2015. 2) The secondary productivity and the P/B ratio of the main groups of macrobenthos in Daya Bay differed significantly. The variation of secondary productivity and P/B ratio of Mollusca, Polychaeta and Crustacean increased during 1988−2004, then decreased during 2004−2015, being consistent with the trend of the whole macrobenthos in Daya Bay. Different from the other groups, the secondary productivity and P/B ratio of Echinoderm showed a decreasing trend during 1988−2015. 3) Generally, the secondary productivity of the macrobenthos had obvious variation in the northwest of the top Daya Bay and Dapeng’ao Bay. The correlation analysis between macrobenthos community and environmental factors indicates that the secondary productivity was significantly affected by the contents of inorganic nitrogen, phosphorus, dissolved oxygen of seawater and organic carbon content of sediment.