The Pythagoras theorem is very famous in the literature of mathematics. It led us to many Pythagorean triples. In this work we have considered all possible Pythagorean triples between 3 to 1000 and generated magic squares, where the sum of entries is a perfect square. The Pythagorean triples are considered in sequential form from number 3 onwards. Fortunately, we have Pythagorean triples for all numbers except number 4. Em total we have 5803 triples. These triples generate 2172 magic squares. These magic squares are written with possible entries. In the second part of the work these magic squares are analysed according to their orders, and found interesting relations with Pythagorean triples. Also, it is observed that there is always a triple with the first element as an even number generating a magic square. These magic squares are written in last section of the work.