Order of taxonomy meta box

Just drag and drop the meta box one time in the left block…. or change the order like 2 or 3 while declaring the meta box Custom Meta Boxes

Add 'normal' as the $context parameter to add_meta_box().
add_meta_box( 'meta-box-id', 'My Meta Box', 'my_display_callback', 'post', 'normal' );

I used register_taxonomy( $taxonomy, $object_type, $args ); so there is no $context parameter.

Ah, my bad. I somehow thought you had a custom meta box. I don’t know of a supported way to relocate the standard custom taxonomy meta box for all users. Altaf’s suggestion to simply drag it into place is a good one, it will persist there for any user who does so.

A possible hacky solution would be to directly manipulate the global $wp_meta_boxes array. Identify your taxonomy’s meta box data in the array and move it to under the “normal” portion of the array. You ought to be able to do so by hooking the “admin_head-post.php” action. Untested, but I believe it would work.

can you explain more?

Sorry, what I presented is just about all I know on the topic. The next step would be to hook that action I mentioned and dump out the array data for examination. You’ll need code to copy your taxonomy meta box data into the “normal” branch of the array and unset the data’s original position in the array.

Finally, I removed the meta box and added that again:

remove_meta_box( 'treediv' , 'taqrir' , 'side' );
add_meta_box('new_treediv', 'Trees...', 'post_categories_meta_box', 'taqrir', 'advanced', 'low', array('taxonomy' => 'tree'));

Note: custom post type is ‘taqrir’ and custom taxonomy is ‘tree’.