How to use Limit in query on my index column without scan all rows?
EXPLAIN is not as smart as one would like.  It provided 42415 without noticing your LIMIT 3.

The important clue that says that it will use the index is the Key column lists the index name.

That query, with that index (I assume ID is a numeric datatype) will touch only 3 rows of the index, then 3 rows of the data.

Two ways to get more info:

EXPLAIN FORMAT=JSON SELECT ...;


or

FLUSH STATUS;
SELECT ...
SHOW SESSION STATUS LIKE 'Handler%';


I would expect to see 2 (3-1) in one or two rows, and not see a number that matches the table size.