To change the content of the new user registration notification email in WordPress, which is sent to said user, we have a specific filter: wp_new_user_notification_email
With this filter, we have access to: recipient’s email address (by default that of the new user created), email subject, email body, email headers.
For example, here is the snippet to change the subject and body of the email:
add_filter( 'wp_new_user_notification_email', function( $wp_new_user_notification_email, $user, $blogname ) {
$message = 'Thank you for registering :)';
$wp_new_user_notification_email['subject'] = sprintf( 'Welcome to %s.', $blogname );
$wp_new_user_notification_email['headers'] = array('Content-Type: text/html; charset=UTF-8');
$wp_new_user_notification_email['message'] = $message;
return $wp_new_user_notification_email;
}, $priority = 10, $accepted_args = 3 );