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Abstract We investigate the kurtosis and skewness of net-baryon number fluctuations in the Polyakov loop extended Nambu–Jona-Lasinio (PNJL) model, and discuss the relations between fluctuation distributions and the phase structure of quark-gluon matter. The calculation shows that the traces of chiral and deconfinement transitions can be effectively reflected by the kurtosis and skewness of net-baryon number fluctuations not only in the critical region but also in the crossover region. The contour plot of baryon number kurtosis derived in the PNJL model can qualitatively explain the behavior of net-proton number kurtosis in the STAR beam energy scan experiments. Moreover, the three-dimensional presentations of the kurtosis and skewness in this study are helpful to understand the relations between baryon number fluctuations and QCD phase structure.