The Beiwagou Pb-Zn deposit, located in the western part of the Liaodong Peninsula, is a carbonate-hosted stratiform deposit with a Pb + Zn reserve of 0.08 Mt @ 4.14% (Pb + Zn). The orebodies occur as conformable layers and lenses and are strictly controlled by strata (the Paleoproterozoic Gaojiayu and Dashiqiao Formations) and lithology (plagioclase amphibolite and dolomitic marble). Given that previous studies have focused only on the mineralization features and mineralogy of deposits, herein, we report in situ trace element analyses of pyrite using LA-ICP-MS, together with in situ sulfur isotopes of pyrite, to constrain the composition, substitution mechanisms, source of sulfur, and sulfate reduction pathways of pyrite in the Beiwagou deposit. Based on pyrite morphology, texture, and chemistry, four pyrite types were identified: subhedral, porous-to-massive pyrite (Py1) related to chalcopyrite; subhedral, porous crushed pyrite (Py2) associated with fine-grained sphalerite; rounded and porous pyrite (Py3) related to the Zn-rich part of the laminated ore; and anhedral, porous-to-massive pyrite (Py4) associated with pyrrhotite, arsenopyrite, sphalerite, and galena. Py1 is characterized by high As, Ag, Cd, In, Au, Cu, and Zn concentrations and low Te, Bi, and Mo concentrations, whereas Py2 has high concentrations of Co and Ni and low concentrations of other trace elements, such as Cu, Zn, Bi, and Te. Py3 is characterized by elevated As concentrations, low Co, Ni, In, W, Te, and Tl concentrations, and varying Pb concentrations, whereas Py4 has low Ag, Cd, In, Zn, Cu, and Mn concentrations and varying W, Co, Ni, Pb, Sb, and As concentrations. Significant correlations between some elements in each pyrite type suggest substitution mechanisms, such as (Zn2+ + Cu2+ + Mn2+ + Cd2+) ↔ 2Fe2+, Ag+ + (Sb)3+ ↔ 2Fe2+, and (Te+ + Ag+) + Sb3+ ↔ 2Fe2+, and the existence of a negative correlation between Co and Ni implies competition between both elements. The strongly positive δ34S values (12.11‰–23.54‰) are similar to that of seawater sulfates and likely result from thermochemical sulfate reduction (TSR). In conclusion, the Beiwagou Pb-Zn deposit is a typical SEDEX deposit and mineralization likely occurred during diagenesis.