I buy food for many companies and I take a special price after I make an invoice with another price, what about this money is it Halal or Haram?

Praise be to Allah, the Lord of the Worlds; and may His blessings and peace be upon our Prophet Muhammad and upon all his Family and Companions. 

It is clear from your question that you are a commission merchant for these companies in buying this food. So, it is unlawful for you to write a price in the invoice that exceeds the actual price with which you actually bought the food. This is because you are an agent and the agent is trusted and any betrayal of this trust is forbidden. Allah Says (interpretation of meaning): {O you who believe! Betray not Allah and His Messenger, nor betray knowingly your Amana (things entrusted to you, and all the duties which Allah has ordained for you).} [8:27]. For more details, please read Fatawa 134924. The agent is entrusted. So, he has no right to deal in what is in his charge except with the permission of his mandator. The scholars of Islam believe that any extra profit the agent gets should be returned to the mandator.Now, you should repent from this act. This repentance is done by first regretting what you did and giving it up completely. You should also have firm resolution not to do it again. You should also return to these companies what you had taken illegally from them. If you fear to face problems while returning it, then you could put it in their account or return it in a way that they do not notice.Allah knows best.