下载letsencrypt工具
git clone https://github.com/letsencrypt/letsencrypt

到下载的目录下
cd letsencrypt/

执行下面命令，给certbot-auto 安装所需要的环境
./letsencrypt-auto

执行下面命令生成证书，生成的过程中会需要你添加txt记录到cloudflare，添加上去就行，
./certbot-auto certonly -d xxxxxx.com -d www.xxxxxx.com --manual --preferred-challenges dns-01 --server https://acme-v02.api.letsencrypt.org/directory -v

生成完之后会成/etc/letsencrypt/live/xxxxxx.com有下面一文件
cert.pem chain.pem fullchain.pem privkey.pem README
其中cert.pem是公钥 privkey.pem是私钥

nginx配置证书如下
listen 443 ssl;
ssl_certificate /etc/letsencrypt/live/xxxxxx.com/fullchain.pem;
ssl_certificate_key /etc/letsencrypt/live/xxxxxx.com/privkey.pem;

apache里面的配置如下

DocumentRoot "xxxxxx/xxx/xxx"
ServerName www.xxxxxx.com
ServerAlias xxxxxx.com
SSLEngine on
SSLProtocol all -sslv2
SSLCipherSuite HIGH:MEDIUM:!aNULL:!MD5
SSLCertificateFile "/etc/letsencrypt/live/xxxxxx.com/cert.pem"
SSLCertificateKeyFile "/etc/letsencrypt/live/xxxxxx.com/privkey.pem"

SSLOptions +StdEnvVars


AllowOverride All
SSLOptions +StdEnvVars