The main man vs. nature conflict in the story has to do with how our bodies betray us.  The premise of the book is that children can be “unwound” for body parts.

An example of the man vs. nature conflict is present when Connor is sent to be unwound and escapes.  He wonders if the police will kill him.

Would they shoot an unarmed kid in the back, he wonders, or would they shoot him in the legs and spare his vital organs. (p. 18)

In this society, organs and body parts are more important than children.  Life itself has no value.  People who are sick or injured and need new organs take them from children who have been chosen to be unwound.

In this society, when people’s bodies betray them (character vs. nature), they can get body parts from the unwinds.

An accident victim who would have died from internal injuries could get fresh organs.  A wrinkled arthritic hand could be replaced with one fifty years younger. (p. 224)

The fact that body parts can be harvested is also a man vs. nature conflict for the unwinds, as well as a man vs. man conflict, because if it was not possible to harvest body parts there would be no need for unwinding.  Of course, there is a also a chracter vs. society conflict here, because the society has passed the Bill of Life and approves the unwinding.

Most of the conflict in Unwind comes from Man versus Society; the future government is very anti-individual and works to "unwind," or harvest, children under the age of eighteen so their parts can be used to help others. There are some examples of Man versus Nature, though, and one comes early when Conner and Risa are fleeing into the woods.

The woods are dense, not just with trees but with tall shrubs and vines, yet there's already a path of broken branches and parted shrubs made by the girl who ran from the bus. They might as well have arrows pointing the police in their direction... she... renews her battle with the dense undergrowth all around her.
(Shusterman, Unwind, Google Books)

The characters are city people, without much experience in the woods, but Conner realizes quickly that the broken branches are an easy tell for the pursuing police. This goes along with the "thick undergrowth," which hampers their progress even as it gives away their position; the forest is almost deliberately trying to get them caught. Using his innate intelligence, Conner figures that the cops will not expect him to use the forest to his own advantage; he climbs a tree and waits for a cop to pass, jumping down to ambush the man and shoot him with his own tranquilizer dart. This shows how the characters take the forest and use it instead of being thwarted by it; they end up having Nature as a natural ally in their fight with Society.