A high-sensitive and specific electrochemical biosensor was designed for simultaneous detection of mercury ion(Hg 2+), lead ion(Pb 2+) and strontium ion(Sr 2+) by oligonucleotide conformational transformation. The biosensor was based on porous anodic alumina(PAA) modified with two oligonucleotide aptamers which could capture Hg 2+, Pb 2+ and Sr 2+, respectively. The aptamers can block [Fe(CN)6] 3-/4- ion conduction in the nanochannels of PAA. In the presence of Hg 2+, Pb 2+ and Sr 2+, the aptamers could bend and wrap around those metal ions to make the nanochannel unobstructed, and then, the redox current of [Fe(CN)6] 3-/4- could be increased. When the biosensor eluted with β-mercaptoethanol(βME), 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid(DOTA) and kryptofix 222(KP) successively, the aptamers stretched and released Hg 2+, Pb 2+ and Sr 2+ in sequence, leading to the re-blockage of nanochannel with the decrease of the redox current. The calibration curves of Hg 2+, Pb 2+ and Sr 2+ were obtained in the range of 0.05—2.50 nmol/L, and the detection limits were 0.013, 0.017 and 0.022 nmol/L, respectively. Furthermore, the biosensor is easily constructed, stable and reusable. It is hopeful to apply in the daily monitoring of harmful metal ions in drinking water or environmental water.