Syrian jets reportedly took off from the Shayrat air base less than 24 hours after it was pounded by 59 Tomahawk cruise missiles.
Mr Trump ordered the strikes on the base in retaliation for the chemical weapons attack on Khan Sheikhoun.
"We do have treaties that we've signed all over the world saying that we're not going to let one nation use weapons of mass destruction, that's what the chemical weapons treaty is all about," Mr Graham told NBC's Meet the Press.
"But I will say this, if you kill babies with conventional bombs it's still a moral outrage."
He added: "Here's what I think Assad's telling Trump by flying from this base: 'F you.'
"And I think he's making a serious mistake, because if you're an adversary of the United States and you don't worry about what Trump may do on any given day, then you're crazy."
During the interview, Mr Graham also said he believed that Mr Trump didn't need to consult with Congress to carry out the strike.
"I think the president has authorisation to use force," he said. "Assad signed the chemical weapons treaty ban. There's an agreement with him not to use chemical weapons."
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