【问题发生环境和相关参数】
(1)OS：Win7 32Bit.
(2)Git：GitHub for Windows 2.0.
下载地址：https://windows.github.com/
(3)Command Shell：Git Shell.
【问题重现描述】
①利用命令“ssh-keygen -t rsa -C "zjrodger@163.com" 生成SSH密匙（id_rsa和id_rsa.pub）后，将本地的“id_rsa.pub”文件中的内容上传到Github上的个人“SSH Keys”管理项中，从而生成一个新的SSH Keys。
②之后，进行本地与Remote Server（Github网站）的连接测试，命令和结果如下所示：
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F:WorkspacesGithub_Workspace> ssh -T git@github.com
Warning: Permanently added 'github.com,192.30.252.131' (RSA) to the list of know n hosts. Permission denied (publickey). |
【问题原因】
在Github for Windows 2.0默认的安装配置中，
SSH的配置文件ssh_config中的“IdentityFile“
与实际情况不相符。
在Github for Windows 2.0上（默认安装情况下），SSH的配置文件ssh_config中的“IdentityFile（其值为密匙的全路径名）”这项信息的内容是“~/.ssh/github_rsa”，如下命令所示：
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Host github.com
StrictHostKeyChecking no
UserKnownHostsFile=/dev/null
IdentityFile=~/.ssh/github_rsa
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(2)实际的情形
而实际上，通过命令“ssh-keygen -t rsa -C "zjrodger@163.com”生成的新的SSH密匙的全路径名为：“~/.ssh/id_rsa”和“~/.ssh/id_rsa.pub”。
注意：~/.ssh/github_rsa 不等于 ~/.ssh/id_rsa
(3)结论
①Git默认安装情况下，ssh_config配置文件中的“IdentityFile”项的值：IdentityFile=~/.ssh/github_rsa
②实际的IdentityFile的值：IdentityFile=~/.ssh/id_rsa
如上所述，Github for Windows 2.0在默认安装情况下，SSH的的配置文件ssh_config中的“IdentityFile”项的值与实际新创建的密匙全路径名不相符，结果导致本地的SSH工具无法找到到正确的密匙，进而无法同已经上传到Github密匙相匹配，结果就出现了“Permission denied (publickey)”这样的错误。
(4)补充
①SSH配置文件ssh_config在自己本地的路径：
C:UsersAdministratorAppDataLocalGitHubPortableGit_6d98349f44ba975cf6c762a720f8259a267ea445etcssh
②密匙文件的存放路径：
C:UsersAdministrator.ssh
③ssh_config的原文件（有误的版本）：
| Host * StrictHostKeyChecking no UserKnownHostsFile=/dev/null Host github.com StrictHostKeyChecking no UserKnownHostsFile=/dev/null IdentityFile=~/.ssh/github_rsa |
为了确保正确性，自己将本机的Github for Window 2.0卸载并且重装了一遍，发现SSH的配置文件ssh_config中的“IdentityFile”依然是“~/.ssh/github_rsa”。
而重装后的密匙文件的存放路径（C:UsersAdministrator.ssh）下，有四个密匙文件，分别是github_rsa和github_rsa.pub，id_rsa和id_rsa.pub，
这样，用户就不用自己新建密匙文件了，只用将“github_rsa.pub”中的内容上传到Github网站的个人SSH管理中即可。
之后，在本地与Remote端进行网络连通性测试，发现可以联通。
这样，考虑到修改软件原有配置信息所带来的隐患，笔者就不推荐自己手动修改SSH的配置文件ssh_config中的“IdentityFile”字段这个方法了。
【解决方法】
方法一：
方法二：
将新生成的密匙文件名字改为“github_rsa”，从而与ssh_config配置文件中的“IdentityFile”项的值相同。
方法三：
方法三：
重装Github for Window 2.0，不用新建密匙文件，而是用Github自带的“github_rsa.pub”文件。
总之，不论方法一，放法二还是方法三，一定要保持新生成的密匙文件的名字同“ssh_config”中“IdentityFile”字段的值一致即可。
【参考文档】
(1)原文链接：http://stackoverflow.com/questions/2127104/permission-denied-publickey-error-using-git-on-windows-7
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If it says "Permission denied (publickey)" you will have to put in a passphrase for your key. Do not be tempted to just press enter...this was what worked for me...it took me five hours to realize that pressing enter made OpenSSH feel that your key was too public so that is why it is denying you from going to the next step. |
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So as mentioned in prior answers, the Permission denied error in Windows is because you are trying to use a key other than id_rsa.
Windows lacks the bells and whistles that Linux and Mac have to try out all your public keys when trying to connect to a server via SSH. If you're using the ssh command, you can tell it which key to use by passing the -i flag followed by the path to the key to use:
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F:WorkspacesGithub_Workspace> ssh -T git@github.com
Warning: Permanently added 'github.com,192.30.252.129' (RSA) to the list of know n hosts. Permission denied (publickey). F:WorkspacesGithub_Workspace> ssh -i ~/.ssh/id_rsa git@github.com Warning: Permanently added 'github.com,192.30.252.129' (RSA) to the list of know n hosts. Enter passphrase for key '/c/Users/Administrator/.ssh/id_rsa': Hi zjrodger! You've successfully authenticated, but GitHub does not provide shel l access. Connection to github.com closed. |