I was assigning the encoded string to window.location.href, thats has limitation of size. It works for small data. For large data, we need to change this way, and i used Blob's, Thanks @dandavis. In Blob's there is no limit of data and we can export large size of files. My previous code is :
var ctx = {worksheet: name || 'Worksheet', table: table.innerHTML}
window.location.href = uri + base64(format(template, ctx))
And now updated code with passing blob is:
var blob = b64toBlob(str, "application/vnd.ms-excel");
var blobUrl = URL.createObjectURL(blob);
window.location = blobUrl;
And the b64toBlob function is here:
function b64toBlob(b64Data, contentType, sliceSize) {
    contentType = contentType || '';
    sliceSize = sliceSize || 512;
    var byteCharacters = atob(b64Data);
    var byteArrays = [];
    for (var offset = 0; offset < byteCharacters.length; offset += sliceSize) {
        var slice = byteCharacters.slice(offset, offset + sliceSize);
        var byteNumbers = new Array(slice.length);
        for (var i = 0; i < slice.length; i++) {
            byteNumbers[i] = slice.charCodeAt(i);
        }
        var byteArray = new Uint8Array(byteNumbers);
        byteArrays.push(byteArray);
    }
    var blob = new Blob(byteArrays, {type: contentType});
    return blob;
}
And its working very fine. I have tested with 55,000 number of rows. Thanks all