It is stated in scriptures that the Supreme Lord has form and has got a spiritual body (sat-cid-ananda vigraha). We too have body but it is called material. With some of our body organs we give out body waste like stool, urine etc. Because we both have similar form does the Lord has body organs like us? If so, then why?
The Vedic literature is full of references to God’s form. For example, it is said that God has no hands or legs but that He can accept anything you offer. Also, it is said that God has no eyes or ears but that He can see everything and hear everything. So, these are apparent contradictions, because whenever we think of someone seeing, we think he must have eyes like ours. This is our material conception. Factually, however, God does have eyes, but His eyes are different from ours. He can see even in the darkness, but we cannot. God can hear, also. God is in His kingdom, which is millions and millions of miles away, but if we are whispering something “conspiracy” He can hear it, because He is sitting within us.
So, we cannot avoid God’s seeing or God’s hearing or God’s touching.
In the Bhagavad-gita [9.26] Lord Krishna says,
patram pushpam phalam toyam yo me bhaktya prayacchati
tad aham bhakty-upahaytam ashnami prayatatmanaa
“If somebody offers Me flowers, fruits, vegetables, or milk with devotional love, I accept and eat it.” Now, how is He eating? We cannot see Him eat, but He is eating. We experience this daily: When we offer Krishna food according to the ritualistic process, we see that the taste of the food changes immediately. This is practical. So God eats, but because He is full in Himself, He does not eat like us. If someone offers me a plate of food, I may finish it, but God is not hungry, so when He eats He leaves the things as they are. God is so full that He can eat all the food that we offer and still it remains as it is. He can eat with His eyes.
As stated in Brahma-samhita(5.32):
angani yasya sakalendriya-vrittimanti pashyanti panti kalayanti ciram jaganti
ananda-cinmaya-sad-ujjvala-vigrahasya govindam adi-purusham tam aham bhajami
“I worship Govinda, the primeval Lord, whose transcendental form is full of bliss, truth and substantiality and is thus full of the most dazzling splendor. Each of the limbs of that transcendental figure possesses, in Himself, the full-fledged functions of all the organs, and eternally sees, maintains and manifests the infinite universes, both spiritual and mundane.”
Even if the organ parts are there they are there just to increase His pleasure in any way possible and not for excretion, digestion, eating etc as there is no need for it.