You can create a second Y axis and associate it with the first (0th) using the xAxis.linkedTo property. Then, in the label formatter of the second axis of the calculations, to get the percentage.
yAxis:[{ }, { labels:{ formatter:function(){ var max=this.axis.linkedParent.dataMax, min=this.axis.linkedParent.dataMin, range=max-min; return ((this.value-min)/(range)*100) + ' %'; } }, linkedTo:0, opposite:true } ]
Double axles | Highchart and Highstock @jsFiddle
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