I have a thousands of data parsed from huge XML to be inserted into database table using PHP and MySQL. My Problem is it takes too long to insert all the data into table. Is
You should put it as said before in a temp directory with a cron job to process files, in order to avoid timeouts (or user loosing network).
Use only the web for uploads.
If you really want to import to DB on a web request you can either do a bulk insert or use at least a transaction which should be faster.
Then for limiting inserts by batches of 100 (commiting your trasnsaction if a counter is count%100==0) and repeat until all your rows were inserted.