What will happen if i change the checkpoint data from bitcoin source code and try to synchronice with blockchain? Suppose i have fully synchronosed bitcoin node running in my local machine and i change its checkpoints data apart from its genesis block and recompile the code. Now what will happen when i try to run the daemon, having older block data residing inside .bitcoin folder. 
Is this what orphan block is?
It will think that the  databases have been corrupted and so it will attempt to redownload the entire blockchain. When it does, it will find that all of the blocks are invalid (because you changed the genesis block) and then it will just do nothing as it is unable to sync what it believes to be a valid blockchain.


  Is this what orphan block is?


No. Orphan blocks are something else entirely and unrelated.