What to do if one ear often gets clogged during later stage of pregnancy?

See ear specialist. Could be any of numerous causes such as wax, infection, congestion common to hormones of pregnancy.
Check with doctor. Sounds like your ear may not be drainage properly. Benadryl (diphenhydramine) or Claritin may help. You should check with your doctor to confirm there is no inner ear infection. If needed, the doc can refer you to an ENT physician.