There is not really a difference in meaning. I would rather use Bevölkerung in a context where I talk about a large amount of people.
die Bevölkerung von Deutschland
die Bevölkerung von Berlin
"Einwohner" can be used for pretty much every amount, even for like a village of 100 people
Die Einwohner des Dorfes
Die Einwohner von Berlin
"Die Bevölkerung des Dorfes" would not be wrong but would sound rather stupid in my opinion.
Einwohner can also be used to describe a single person living somewhere as in "der Einwohner"