"Are they on your desk?" is the Engpsh translation of "它们在你的桌子上面吗?"
The phrase "on your desk" is a prepositional phrase indicating location. The preposition "on" shows that the noun "they" is in contact with and physically resting on the surface of the noun "desk."
Examples:
"Are your keys on the desk?"
"Is the book on your desk?"
"The pen is on the desk."
翻译：
"你的钥匙在桌子上吗？"
"书在你桌子上吗？"
"钢笔在桌子上。"