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Using the QCD factorization approach, we investigate the large branching ratios of B →ηK* decays and the SφKs anomaly of B →φKs decay in the two Higgs doublet model Ⅲ With the contributions of flavour-changing neutral current mediated by the neutral Higgs bosons H0, h0 and A0 at the tree level, we provide a coherent resolution to these anomalies within the constrained parameter spaces, which are 120 < |λbsλss| < 136. This will be really interesting in searching for the signs of new physics.