China has implemented the domestic emission control area (DECA) policy for shipping in different phases, such as DECA1.0 (2016–2018) and DECA2.0 (2019). This study aimed to examine the effects of cleaner ship fuels on air pollutants. The long-term online field measurements of SO2, NOX, CO, and PM2.5 have been carried out at Chongming Island, located at the cross section of the Yangtze River and the East China Sea, to observe the variation driven by the evolution of different-phased DECA policy during 2013–2019. Our results revealed that SO2 showed an evident declining trend in different seasons. Meanwhile, on-line hourly elemental vanadium and nickel concentrations in PM2.5 at Chongming Island and two other inland sites in Shanghai were measured. There were covariations and a decreasing gradient in the vanadium concentration from the Chongming Island site to the coastal site to the inland site in Shanghai. In retrospect to 2015, i.e., before DECA, the vanadium concentration had a reduction of 5.8% for DECA1.0 (2016–2018) and one of 60–70% for DECA2.0 (2019). The observed reduction was confirmed by the estimated decrease in ship emission amount of SO2 and vanadium around the Shanghai port after DECA policy. The annual average concentrations of vanadium and nickel in Chongming Island were still 5.69 ng/m3 and 3.1 ng/m3 even after DECA2.0, respectively. The ambient concentration of metals at the ecological Island could reduce the most in future cleaner fuel oils scenario. Our study provided the evidence for the environmental benefit of clean fuel oil and indicated the need of a full-scale switching to a stricter ship ECA policy in future.