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You can scale the height of the second chart to match the ratio of the # of elements in the two charts.
Chart.js requires a container around the canvas to allow dynamic resizing so you’ll need to add that to the html also.
I needed to set maintainAspectRatio: false
for this to work
// scale second chart based on ratio of data to the first
var fiddleFactor = 1.05; // determined by guesswork. Basic ratio is slightly off.
var ratio = data2.labels.length * fiddleFactor / data1.labels.length;
var container1Height = parseInt(document.getElementById("container1").style.height);
// update height of second chart
document.getElementById("container2").style.height = container1Height * ratio + 'px';
<div id="container1" class="chart-container" style="position: relative; height:300px;">
<canvas id="myChart"></canvas>
</div>
<div id="container2" class="chart-container" style="position: relative; height:300px;">
<canvas id="myChart2"></canvas>
</div>
Source:stackexchange.com