The formation of authigenic carbonate in marine environments represents a process that buffers ocean chemistry and atmospheric carbon dioxide levels. The isotopic composition of calcium (δ44/40Ca) in authigenic carbonate can be used to investigate the calcium (Ca) cycle, seawater chemistry, and diagenesis of carbonate rocks, archiving key information on the evolution of the Earth's surface environments. Laboratory experiments have shown that Ca isotopic fractionation during carbonate precipitation – the basis of the δ44/40Ca proxy – is mainly determined by both mineral phase and precipitation rate. However, the precipitation rate of submarine authigenic carbonate is much lower than rates in laboratory experiments. This study investigated the Ca isotopic composition of pore water and carbonate nodules collected from two gravity piston cores and one push core from the Haima seeps in the northern South China Sea. Methane fluxes calculated for the three cores range from 12 to 134 µmol cm−2 yr−1. The core with intermediate methane flux showed evidence of aragonite precipitation, while high-Mg calcite was the dominant mineral phase in the other two cores as indicated by Mg/Ca and Sr/Ca ratios of pore water. Numerical modeling of pore water geochemistry revealed that: (1) precipitation rates of carbonate per unit reactive surface area range from 0.05 to 21 µmol m−2 h−1, which is one to three orders of magnitude lower than rates in precipitation experiments; (2) Ca isotopic fractionation for aragonite precipitation is –1.8 ± 0.3 ‰, close to the reported equilibrium isotopic fractionation in precipitation experiments; and (3) Ca isotopic fractionation for high-Mg calcite precipitation is similar for the two cores (−0.9 ± 0.3 ‰ and −0.8 ± 0.3 ‰), although the modeled precipitation rates differed by two orders of magnitude. These results indicate that mineralogy rather than precipitation rate is the primary control on Ca isotopic fractionation during carbonate precipitation at seeps, resulting in lower δ44/40Ca values of aragonite (0.91±0.06 ‰, N = 4) than of high-Mg calcite (1.41±0.04 ‰, N = 9) reported relative to NIST SRM915a. This study documents distinguishable Ca isotopic fractionation during the formation of methane-derived high-Mg calcite and aragonite, providing fundamental parameters for further exploration of the calcium isotopic composition of marine authigenic carbonates in the geological record.