Yes you can change the theme css file according to you.
If you want more customization like changing the icons when open, when close etc then you can do it in jquery
$('#jstree-api').jstree({
'core': {
'data': jsonData
},
"types": {
"child": {
"icon": "glyphicon glyphicon-leaf"
},
"root": {
"icon": "glyphicon glyphicon-folder-close"
},
"default": {
"icon": "glyphicon glyphicon-folder-close"
}
},
"search": {
"case_insensitive": true,
"show_only_matches": true
},
"plugins": ["search", "themes", "types"]
});
$('#jstree-api').on('open_node.jstree', function (e, data) {
data.instance.set_icon(data.node, "glyphicon glyphicon-folder-open");
}).on('close_node.jstree', function (e, data) { data.instance.set_icon(data.node, "glyphicon glyphicon-folder-close"); });
Here is a series of articles on jsTree you can follow if you want.