CentOS7, Fedora27,

Please,

• paste the output of SHOW CREATE TABLE <tablename> and SHOW INDEX IN <tablename>;
• paste the example of the wrong results that you are getting (you don't need to paste 18M rows, a few ones that show wrong values will do);
• clarify how ALTER TABLE is involved (since you set it in the Component field);
• attach your cnf files;
• and yes, please upload your test data to ftp.askmonty.org/private.

Thank you for replying. And Sorry for late reply. I had caught a cold and not to confirm your message during a few days.
*

• paste the output of SHOW CREATE TABLE <tablename> and SHOW INDEX IN <tablename>;**

I put mysqldump data on my server. Please get it from my server. "word" table is over 180M records.
here is download URL
http://www.qurataro.com/wikipedia_20170601.sql.bz2

• paste the example of the wrong results that you are getting (you don't need to paste 18M rows, a few ones that show wrong values will do);
  *
  select C, A from table order by C, A ASC;
  Case : 170M records(success)
  1,4
  1,20
  1,3
  Case : 180M records(wrong)
  1,0
  1,0
  1,0

• attach your cnf files;*
  I use default setting of cnf files.(my.cnf and under my.cnf.d folder) I don't change it.

Thanks. So, I assume the table is `word`, but which column in your example is `C` and which is `A`?
I tried several variations, but I'm not getting the result that you've described. Also, the table structure is different there, at least INT columns are INT(8) and not INT(12) as you described. Is it possible that you mixing results and expectations from different instances?

Another thing hints at that – this cannot be right (or cannot be success):

select C, A from table order by C, A ASC;

1,4

1,20

1,3

The result is not ordered by A here as it should.

sorry, I ought to write real value name, And sorry for late reply.

select subword_num, word_num from word order by subword_num, word_num ASC;
TRUE
1,4
1,20
1,3

FALSE
1,0
1,0
1,0