Woocommerce custom taxonomy order

You may consider using the get_terms() function to generate a list of the items in a custom taxonomy. I’m sure there are other good ways of doing this, but there are plenty of parameters here you can try out to get the order you need.

    $terms = get_terms( 'custom_taxonomy_here', 'orderby=count&hide_empty=0' );
        if ( ! empty( $terms ) && ! is_wp_error( $terms ) ){
        echo '<ul>';
        foreach ( $terms as $term ) {
            echo '<li>' . $term->name . '</li>';
        }
        echo '</ul>';
    }

In the example above, orderby orders the terms by their count (but there are other arguments for a different order) and hide_empty to display terms whether or not they are associated with a post.