Just keep calling zip.file().

Look at the example from their documentation page (comments mine):

var zip = new JSZip();

// Add a text file with the contents "Hello World\n"
zip.file("Hello.txt", "Hello World\n");

// Add a another text file with the contents "Goodbye, cruel world\n"
zip.file("Goodbye.txt", "Goodbye, cruel world\n");

// Add a folder named "images"
var img = zip.folder("images");

// Add a file named "smile.gif" to that folder, from some Base64 data
img.file("smile.gif", imgData, {base64: true});

zip.generateAsync({type:"base64"}).then(function (content) {
     location.href="data:application/zip;base64," + content;
});

The important thing is to understand the code you've written - learn what each line does. If you do this, you'd realize that you just need to call zip.file() again to add another file.