Itchy ears?

My dog bailey (jack russel and beagle mix age 3) has been shaking her head and then leaning it to one side... is it okay to stick my finger in her ear and scratch it like I would mine??? It happens from time to time (maybe every 3-5 months) I just want to know if I’m doing something that doesn’t hurt her in the long run, because while I’m doing it at first she’s okay with it and then she asks like it bothers her (no biting or anything just done with the service I provided lol ) and she stops shaking her head and leaning it...