Objective To evaluate the dynamic changes of residue level of malachite green (MG) and nitrofurans, including relevant metabolites, in turbot, snakehead fish and Chinese perch (i.e., “two types of prohibited veterinary drug abused in three kinds of fishes” issue) in Shanghai from 2008 to 2018, and to conduct dietary risk assessments of Shanghai residents. Methods Based on risk monitoring project from 2008 to 2018, a margin of exposure (MOE) approach was applied to evaluate human health risk according to the daily food consumption investigation of local residents. Results The average unqualified rate of two types of prohibited drugs abused in three kinds of fish was 19.0%(148/779) in the past 11 years, which fluctuated in a downward trend. The unqualified rate dropped from 33.7%(30/89) in 2008 to 3.6%(2/55)in 2018 with a 89.3 % declining range. In terms of different fish species, the unqualified rates of MG and nitrofurans in turbot, snakehead fish and Chinese perch were 42.6%(100/235), 8.6%(21/244) and 9.0%(27/300), respectively. Nitrofuran abuse problem (17.8%,139/779) outweighed that of MG (1.2%,9/779) in the past 11 years. The chronic risks of dietary intake of MG and nitrofurans from fishes were classified at very low level (MOE>10⁴), of which MOE were 1.7×10⁶ and 1.6×10⁶, respectively. Conclusion The malachite green and nitrofurans abuse in three kinds of fish Shanghai was improved in general. Shanghai residents did not face a possible chronic health risk either from MG or nitrofurans in fishes; however, authorities should continuously keep tight supervision and control of the MG and nitrofurans as prohibited veterinary drugs.