Next generation neutrino telescopes are highly anticipated to boost the development of neutrino astronomy. A multi-cubic-kilometer neutrino telescope, TRopIcal DEep-sea Neutrino Telescope (TRIDENT), was proposed to be built in the South China Sea. The detector aims to achieve ∼ 0.1 degree angular resolution for track-like events at energy above 100 TeV by using hybrid digital optical modules, opening new opportunities for neutrino astronomy. In order to measure the water optical properties and marine environment of the proposed TRIDENT site, a pathfinder experiment was conducted, in which a 100-meter-long string consisting of three optical modules was deployed at a depth of 3420 m to perform in-situ measurements. The central module emits light by housing LEDs, whereas the other two modules detect light with two independent and complementary systems: the PMT and the camera systems. By counting the number of detected photons and analyzing the photon arrival time distribution, the PMT system can measure the absorption and scattering lengths of sea water, which serve as the basic inputs for designing the neutrino telescope. In this paper, we present the design concept, calibration and performance of the PMT system in the pathfinder experiment.