Writing an apt proxy conf file /etc/apt/apt.conf.d/proxy.conf
as below.
Acquire::http::Proxy "socks5h://127.0.0.1:1080";
Acquire::https::Proxy "socks5h://127.0.0.1:1080";
Acquire::socks::Proxy "socks5h://127.0.0.1:1080";
And the proxy settings will be applied the next time we run apt.