As far as I know, if you want to hosted the Codeigniter in the IIS, you need to add some special url rewrite rule to let your application work well.
I suggest you could install the url rewrite extension for the IIS firstly.
Then I suggest you could try to add below rule into the web.config.
  <system.webServer>
    <rewrite>
      <rules>
          <rule name="Index">
          <match url="^(.*)$" />
          <conditions>
            <add input="{REQUEST_FILENAME}" matchType="IsFile" negate="true" />
            <add input="{REQUEST_FILENAME}" matchType="IsDirectory" negate="true" />
          </conditions>
                <action type="Rewrite" url="index.php/{R:1}" />
        </rule>
      </rules>
    </rewrite>
  </system.webServer>