A silicon nanowire bio-chip structure and a manufacturing method thereof. The structure comprises a semiconductor substrate (1), a SiO2 insulating layer (2) formed on the semiconductor substrate, a polysilicon layer (3) formed on the SiO2 insulating layer (2) and a structural layer formed on the polysilicon layer (3); wherein, the polysilicon layer (3) comprises a patterned silicon nanowire array (4); the structural layer includes a SiON layer, a TaN and/or Ta2O5 layer (6) from bottom to top, the TaN and/or Ta2O5 layer only covers surface of each silicon nanowire in the silicon nanowire array. The silicon nanowire array is prevented from being polluted during preservation and use, and the pollutants of Na ions, K ions, Fe ions, Cu ions and Ca ions as well as the effects of chemical factors including the PH value are blocked during biological detection, thereby achieving the high stability of detection.