Add twig template to custom entity

/**
* Implements hook_theme().
*/
function mymodule_theme() {
 return [
   'my_entity' => [
     'render element' => 'elements',
   ],
 ];
}
 * Implements hook_preprocess_HOOK().
*/
function my_module_preprocess_my_entity(&$variables) {
 $variables['content'] = [];
 foreach (Element::children($variables['elements']) as $key) {
   $variables['content'][$key] = $variables['elements'][$key];
 }
}

Add twig template my_entity.html.twig to /templates directory

<div{{ attributes.addClass('my-entity') }}>
 {% if content %}
   {{ content }}
 {% endif %}
</div>