You're going to have to get out of what seems to be the habit of using your thumb to grip the neck too hard. This is a far too common an occurrence, and leads to your symptoms. It often ends in RSI., which as a guitar or bass player, you do not want!
Why does my fretting hand hurt bass?
A “dulling” pain where soreness is felt in the fret hand wrist, similar to a mild sprain, and takes anywhere from a few hours to a few days to heal. ... The reason you're getting wrist pain is probably because your new bass has a thin neck on it.
Is it normal for your fingers to hurt after playing bass?
When first playing a string instrument, the relatively soft tissue on the tips of your fingers experiences repeated blunt trauma , according to a 2011 study. The trauma results from making constant, repetitive contact with the harsh material of the strings.