Update:
I have successfully registered the certificate and make it work.
After trying several tutorials, IMO this link below is the cleanest way. The other tutorial at my first post is okay too, but required more manual work.
Nginx and Let’s Encrypt with Docker in Less Than 5 Minutes | by Philipp | Medium
Things I have tried:
Uninstall nginx in local machine, only use the one provided by docker.
For newcomers like me, remember to use flag --staging when execute "certonly" command to test whether the process is successful or not to avoid the limit time of registration of one domain. (if using the bash script from the link above, set "staging=1" at line 12.
Special Thanks to @rg305 for his valuable support. 