Inland river ships (IRSs) use diesel with a lower sulfur content and emit relatively low emissions, making it challenging to monitor their emissions. Sniffer monitoring equipment was installed from August 2020 to June 2022 at the Gezhou Dam of the Yangtze River and monitored emissions from 8,238 IRSs passing through the lock. We partnered with the maritime department to select 100 ships passing through the lock to extract fuel oil samples for direct fuel sulfur content (FSC) detection, which determined the actual FSC of the passing ships. The monitoring data from these 100 ships indicated that the relative error of the SO2 emission factors (EFs) and FSC results is significant at the 10-parts-per-million level. The monitoring data from the remaining 8,138 ships showed that the EFs of NO, NO2, PM2.5, and PM10 were 24.02 ± 16.92 g kg−1, 10.30 ± 18.08 g kg−1, 0.72 ± 0.60 g kg−1, and 0.92 ± 0.70 g kg−1, respectively. The NOx EFs of container ships are higher than those of other ship types, while the PM EFs for different ship types do not significantly differ. Based on these EFs, we calculated the average emission rates for different types of ships passing through locks, which is a real-time measurement method for estimating ship emissions. In addition, a comparison of ship EF measurements over the past 20 years revealed that EF values for SO2, NOx, and PM exhibited a downward trend, with the calculated results of the current study determined to be the lowest numerical level.