In port transportation, the detection of sulfur content in vessel fuel has always been the focus of the maritime sector. However, the existing detection methods are tough to achieve remote monitoring effectively. This paper proposes a remote measuring method of CO2 and SO2 in vessel exhaust based on hyperspectral imaging technology. The Fourier transform interference hyperspectral imaging technology, and hyperspectral three-dimensional low-rank optimization technology is developed, which can effectively solve the low-concentration detection problems in open light path and complex environment. We perform the sulfur content detection tests for the fixed and random vessel day and night at Dongjiang Wharf of Tianjin Port. The Fourier transform interference hyperspectral imaging technology has been developed for remote exhaust detection under the complex open light paths. The hyperspectral data is preprocessed by hyperspectral imaging three-dimensional low-rank optimization technology. Finally, the accurate detection of sulfur content in vessel fuel has been analyzed accurately using partial least square (PLS) stoichiometry technology and a radiation transmission model according to the atmospheric radiation situation. The detection of fixed and random vessels filled with high sulfur fuel in day and night environments is accomplished. The detection distance is more than 1000 meters, and the single detection time is less than 3 s. The results are consistent with the data held by the maritime department, which verifies the feasibility of remote passive measurement of sulfur content in vessel fuel based on hyperspectral imaging technology.