Copper-zinc isotopic excursions in carbonate sedimentary successions are used to trace oceanic chemistry fluctuations that occurred in the geological past. However, whether carbonate sediments can accurately record the Cu-Zn isotopic compositions of coeval seawater is still a matter of debate. We analyzed the Cu-Zn isotopic compositions of well-characterized methane-derived carbonates from drill cores in the South China Sea to decode the effect of the sedimentary environment on Cu-Zn isotopic fractionation. All seep carbonates have uniform δ65Cuauth values (the per mil deviation of the 65Cu/63Cu ratio from the NIST 976 standard; −0.22‰ to 0‰) independent of the sedimentary environment. In contrast, the δ66Znauth values (the per mil deviation of the 66Zn/64Zn ratio from the JMC-Lyon standard) of seep carbonates that precipitated from bottom seawater (intense methane seepage; 0.59‰ to 1.03‰) are significantly higher than those that formed in pore-water environments (low methane flux; −0.07‰ to 0.41‰). This evidence implies that changes in sedimentary environments can affect the Zn isotopic fractionation of carbonate sediments. Furthermore, the strong sedimentary environment-dependent Zn isotopic fractionation proves the validity of using Zn isotopes as a robust proxy for tracing paleo-methane seepage intensity caused by gas hydrate dissociation.