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You can align y-axis across multiple charts by setting the margin property. The margin value has to be calculated based on the bounds of y-axis as shown in the code below –

var axisYBoundMax = 0;
for (var i=0; i<charts.length; i++) {
  axisYBoundMax = Math.max(axisYBoundMax, charts[i].axisY[0].bounds.x2);

for(var i = 0; i < charts.length; i++) {
  charts[i].axisY[0].set("margin", axisYBoundMax - (charts[i].axisY[0].bounds.x2 - charts[i].axisY[0].bounds.x1));

Please take a look at this JSFiddle for complete working code.

Align Y-axis across Multiple Charts

Manoj Mohan
Team CanvasJS