A pentaerythritol core, phosphonic acid terminated dendrimer, its preparation method and application are provided. A preparation method of the pentaerythritol core, phosphonic acid terminated dendrimer (PETA-ADA-12PO3H2) comprises steps of processing Michael addition reaction on pentaerythritol tetraacrylate (C(CH2OCOCH2=CH2)4) and alkylidene diamine (NH2CH2(CH2)nNH2), wherein n is an integer from 1 to 5, so as to obtain pentaerythritol core, amino group terminated dendrimer, and modifying the amino group by methylene phosphonic acid to obtain the PETA-ADA-12PO3H2 having a chemical formula of C[CH2OCOCH2CH2N(CH2PO3H2)CH2(CH2)nN(CH2PO3H2)2]4, wherein n is an integer from 1 to 5. The PETA-ADA-12PO3H2 has a high calcium tolerance, and excellent inhibiting efficiency of calcium carbonate, calcium sulfate and barium sulfate, which is applied in inhibiting the formation and deposition in the industrial water systems of circulating cooling water, oilfield flooding and reverse osmosis, and particularly suitable for water treatment with high calcium tolerance.