Teach HM Cut to a Pokemon and use it on the tree.
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bidoof and bibarel can cut trees
You have to get the hm, then, you have to beat bugsy, the Azalea town gym leader. After that, teach it to one of your Pokemon so you can cut down trees.
You have to get the HM01(cut) , teach it to a Pokemon and when you're facing the a tree to cut down open the Pokemon team menu and click on the Pokemon that knows cut and select the cut option. You also need the second gym badge
You get HM01 Cut from Ilex Forest. Use that to cut down trees.
HM01 Cut