How can I configure a custom CloudWatch alert for my Ec2 instance ?

Without an agent/application or scheduled script there is no way for the operating system metrics to be sent to cloudwatch and therefore no way to set an alert.

Most commonly customers install the cloudwatch agent to send OS metrics + custom metrics to cloudwatch. If using an AMI with SSM already installed the agent can be deployed via SSM

To create custom metrics without using CloudWatch Agent, you must use AWS CLI or AWS SDK to create a script to fetch the necessary values.
If the only metrics you want to get are disk and memory, it would be easier to include CloudWatch Agent than to create a script.