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A portable X-ray Fluorescence Spectrometer (XRF) can be used for field analysis with the advantages of rapidity and non-destruction; the applications of hand-held XRF in in-situ analysis of cobalt-rich crust chunks and core are described. The calibration curve for cobalt-rich crusts was established using national certified reference materials such as GBW 07337, GBW 07338 and GBW 07339. The proposed method has been validated by analyzing certified reference materials; the relative standard deviation was 0.3%-3.0%, which is appropriate for analysis of cobalt-rich crust in field. The hand-held XRF was utilized for in-situ analysis of cobalt-rich crust chunks and drilling core in marine exploration. A comparison of the results from in-situ analysis of dried crust chunks and those obtained from the hand-held XRF instrument after pressed powder sample preparation is presented, and good consistencies were found for the elements of interest. The data of in-situ analysis of crust core was evaluated by comparing with that obtained from laboratory testing after powder was layered artificially; the results based on two different methods indicate that distribution features of Mn, Fe, Co, Ni and Cu are similar. The methodology has been proved to be an effective method for in-situ analysis, which can meet the need of fast evaluation of cobalt-rich crusts resources, meanwhile, the proposed method, is appropriate for distribution research of Mn, Fe, Co, Ni and Cu in original cobalt-rich crust, which is helpful for the study of mineralization in different metallogenic stages of the crust.