Mr Castro's speech to a summit of leftist leaders in Venezuela was broadcast by state-run television on Sunday evening.
Before taking office, Mr Trump threatened to torpedo the detente between the former Cold War foes unless a "better deal" could be struck, without providing details. The White House said last month it was in the middle of "a full review of all U.S. policies towards Cuba."
Raul Castro said: "The new agenda of the U.S. government threatens to unleash an extreme and egotistical trade policy that will impact the competitiveness of our foreign trade; violate environmental agreements ... hunt down and deport migrants."
He said migration was due to growing inequality and poverty caused by an unjust international economic system and that a wall along the Mexican border was therefore "irrational" and aimed at all Latin Americans, not just Mexicans.
"You can't contain poverty, catastrophes and migrants with walls, but with cooperation, understanding and peace," Mr Castro said.
The two close neighbors have since restored diplomatic ties and signed cooperation agreements.
Mr Trump said last month after having dinner with Florida Senator Marco Rubio, a vociferous foe of detente, that he and Rubio had similar views concerning Cuba.
Mr Obama, a Democrat, used executive orders to circumvent the longstanding US trade embargo on Cuba and ease some restrictions on travel and business. The embargo can only be lifted by the US Congress, which is controlled by Republicans.
Travel to the Caribbean island from the United States has increased, with the start of direct flights and cruises and roaming agreements signed, but no manufacturing or significant trade deals have yet been agreed.