Think of it as 'pain is happening in my ear'. हो रहा है is the verb होना (to be) in continuous form (is being/happening). You see these continuous forms fairly often in Hindi, like with "I am hungry": मुझे भूख लग रही है (I am feeling hunger).

कानों instead of कान

Where there's a postposition (में), the direct case (मेरा कान) changes to oblique case (मेरे कान में)

https://en.wikibooks.org/wiki/Hindi_Lessons/Lesson_7

You could translate it literally as "pain is being". Thus, "in my ear pain is being" would be "my ear is aching"