Hi@akhtar,
You can use a network interface in your EC2 instance. It will allow you to use a subnet in a VPC as shown below. 
# Create a linux instance in the subnet
instances = ec2.create_instances(
 ImageId='ami-0de53d8956e8dcf80',
 InstanceType='t2.micro',
 MaxCount=1,
 MinCount=1,
 NetworkInterfaces=[{
 'SubnetId': subnet.id,
 'DeviceIndex': 0,
 'AssociatePublicIpAddress': True,
 'Groups': [securitygroup.group_id]
 }],
 KeyName='ec2-keypair')