。
It seemed she thought it only natural for him to have his own way.
Literal
She [topic-は] [he [subject-が] [own-自分の] desire's-way [adverbial-に] do [topic-のは] natural matter [quotative-と] is-thinking] [as-ように] (it) seemed.
Multiple layers. The deepest proposition 彼が自分の思い通りにする ('he does as 自分 [= he himself] pleases') is wrapped with のは ('as for the act of'), evaluated as 当然の事 ('a natural thing'), marked with と as the content of 考えている. That whole impression is then framed with ~ように思える — 'it gave the impression that ~.' Note 思える is the spontaneous-potential of 思う ('one can't help but think'). 自分 here refers back to the embedded subject 彼.