Shale gas exploration and development carry the risk of causing groundwater contamination and enhancing the greenhouse effect through methane leakage. Identifying the source of abnormal methane in groundwater of shale gas development areas is becoming a research hotspot in the fields of groundwater and climate change. This paper reviews the traditional methodology in identifying sources of methane and its deficiency in groundwater application. Then potential and advantages of using noble gases were discussed on how to overcome these limitations of the traditional method. Finally, based on noble gas, the current application status and future challenges of methane source identification in groundwater were analyzed. It can be summarized as: (1) due to chemical and/or microbial processes in the aquifer system, the traditional methodology for methane source identification, which utilizes molecular and isotopic compositions of hydrocarbon gas, has multiple interpretationsand large uncertainties; (2) the non-reactive nature and well-characterized isotopic compositions of noble gases in the atmosphere, hydrosphere, and crust, make noble gases ideal indicators of the sources of methane in groundwater. Moreover, the mechanism of formation and release of crustal noble gas prevent shale gas signatures from being interfered with by natural gas; (3) the key scientific tasks surrounding the use of noble gases for methane source identification include quantitatively separating the components of atmosphere-derived, mantle-derived, and crust-derived noble gases from the bulk noble gases in groundwater. It quantifies the solubility fractionation of noble gases induced by water-gas interaction during methane migration to the aquifer. The application of noble gases can bring a new perspective to tracing the source of methane in groundwater and is of great significance to the protection of groundwater quality in shale gas development areas and mitigation of climate change.