Does he get ear infections? Or is there a lot of dark colour wax always there? If you find you need to clean his ears often, then maybe look at why. My Lola always had ear infections and build up of wax, she was always getting antibiotic drops and ear cleaners until we found out she has a thyroid issue and since being treated for thyroid she no long has wax build up and raw itchy ears any more.
If your little one is this terrified, maybe leave the cleaning for a week or two then when he is very relaxed, say almost asleep, put some of the solution onto a cotton wool ball and gently clean his ears, do it slowly and carefully and give him a reward when you are finished. He is either in pain or something has happened to make him freak out, so you are going to have to spend a bit of time building his trust and confidence again with you putting things in his ears.