How can I change the value of min word length for specific query in fulltext search?
Short answer:  Not possible.

Long answer...

That setting is used when any MyISAM FULLTEXT index is being built.  You should change to InnoDB, in which case innodb_ft_min_token_size is the variable to set.  (It defaults to 3.)

If you change the setting after the index is built, it has no effect on existing indexes or queries using those indexes.

The only way to change it is to (1) change it in my.cnf, then (2) rebuild the index on any table for which you want the new length.