But I understand what he's saying.

Literal

But, I [topic-は] he [of-の] say thing [subject-が] understand.

The clause 彼の言うこと 'what he says' is a noun-modifying construction where the subject 彼 takes の instead of が — a standard feature of Japanese relative clauses, where の can substitute for が when the clause is embedded as a modifier. 分かる is an intransitive verb whose logical object is marked with が, not を: 'X ga wakaru' literally 'X is understood,' with the understander being the topic.