When I changed AWS::ApiGateway::Method properties by AWS SAM template and deployed it. but I noticed that change was not reflected until I deploy API manually from AWS management console. I think it is because I didn't change the resource of AWS::ApiGateway::Deployment and AWS::ApiGateway::Stage on the template.(The deployment history of AWS::ApiGateway::Stage was not updated.)
How can I reflect the change when I trigger sam deploy?
No, you have to manually deploy the api from the console :) it's a limitation at the moment.