Objective To comprehensively and systematically analyze mercury concentration and associated characteristics in aquatic products, and to evaluate the degree of pollution and make a dietary mercury exposure risk assessment. Methods Based on a large amount of nationwide data regarding mercury contents of aquatic products published during the last decade, we analyzed the characteristics of mercury contents in aquatic products and further made a health risk assessment using Monte Carlo simulation combined with residents’ food consumption data. Results The number of valid samples was up to 19 531. Generally, mercury concentrations in aquatic products were far lower than national standard values and marine products were obviously higher than freshwater products. Mercury concentrations of some fish, marine shellfish and freshwater crustaceans were even up to slight to moderate polluted level. Intriguingly, mercury contents of seawater farmed fish were significantly higher than wild fish. Dietary exposure risk was below the PTWI established by JECFA while all kinds of aquatic products for women aged 45 or older and people aged 6 to 17 were at higher risk with P95 exposure level. Conclusion The mercury concentration of aquatic products is relatively low and its associated health dietary risk is acceptable in spite of higher risk for specific population. More attention should be paid on fish breeding model around the South China Sea.