For the purpose of monitoring the emission compliance of navigating ships in key waters of Shanghai, the present study adopts a sniffing method involving an unmanned aerial vehicle (UAV) platform-based ship exhaust mini-sniffing system measuring the concentrations of SO2 and CO2 within the plumes of navigating ships, then estimating the fuel sulfur content (FSC) of ship. The proposed method aims to provide a low-cost, non-contact method to assess the compliance level of FSC of navigating ships. Experimental tests were performed on ships in the Yangtze River Estuary and the core section of the Huangpu River, the key waters of Shanghai. 679 ships were monitored in the experiment, of which 13 ships were monitored by UAV with FSC greater than 0.5% (m/m). Due to the prevention and control of the COVID-19 pandemic, 8 monitored ships were intercepted by maritime law enforcement(MLE), and fuel oil samples were collected and analyzed in laboratory. The results show that the FSC of the 8 ships was greater than the limit of 0.5% (m/m). Finally, the monitoring results are comprehensively analyzed according to different ship lengths, types, nationalities and water areas. From the experimental results, it can be concluded that the FSC of Chinese cargo ships with length in the range of 80–160 m is more likely to exceed the standard 0.5%(m/m). The probability of exceeding the standard 0.5%(m/m) of navigating ships in the Yangtze River is higher than that of the Huangpu River. Overall, the presented study provides a reference for ship supervision in emission control areas (ECAs), which can improve the efficiency of MLE.