What is the fastest way to empty s3 bucket using boto3?

Just use aws cli.

aws s3 rm s3://mybucket --recursive

Well, for longer answer if you insists to use boto3. This will send a delete marker to s3. No folder handling required. bucket.Object.all will create a iterator that not limit to 1K .

import boto3    
s3 = boto3.resource('s3')
bucket = s3.Bucket('my-bucket')
# suggested by Jordon Philips 
bucket.objects.all().delete()