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A generalized Brans-Dicke (GBD) theory in the framework of Palatini formalism are proposed in this paper. We derive the field equations by using the variational approach and obtain the linearized equations by using the weak-field approximation method. We show various properties of the geometrical scalar field in the Palatini-formalism of GBD theory: it is massless and source-free, which are different from the results given in the metric-formalism of GBD theory. Also, we investigate the polarization modes of gravitational waves (GWs) by using the the geodesic deviation method and the Newman-Penrose method in the Palatini-GBD theory. It is observed that there are three polarizations modes and four oscillation in the Palatini-GBD theory. Concretely, they are the two transverse tensor ($+$) and ($\times$) standard polarization modes, and one breathing mode (with two oscillation). The results of GWs polarization in the Palatini-GBD theory are different from that in the metric-GBD theory, where there are four polarizations modes: the two standard tensorial modes ($+$ and $\times$), a scalar breathing mode, and a massive scalar mode that is a mix of the longitudinal and the breathing polarization. Comparing with the Palatini-$f(\tilde{R})$ theory and the General Relativity, we can see that the extra breathing mode of GWs polarization can be found in the Palatini-GBD theory. At last, the expression of the parameterized post Newton (PPN) parameter is derived, which could pass through the experimental test.