How can i Use drupal 8 CMI between two different sites? I think, normally the CMI works between cloned sites, not different sites. Is there any way to do that with CMI ? or still we hardly depends the features module ?
I'm afraid you are right, configuration management is for different instances of a same site. According to the Drupal 8 CMI documentation,


  The Configuration Manager module in Drupal 8 provides a user interface
  for importing and exporting configuration changes between a Drupal
  installation in different environments, such as Development, Staging
  and Production, so you can make and verify your changes with a
  comfortable distance from your live environment.


The same idea appears in this article, 


  Perhaps the most important concept to understand is that the
  configuration system is designed to optimize the process of moving
  configuration between instances of the same site. It is not intended
  to allow exporting the configuration from one site to another. In
  order to move configuration data, the site and import files must have
  matching values for UUID in the system.site configuration item. In
  other words, additional environments should initially be set up as
  clones of the site. We did not, for instance, hope to facilitate
  exporting configuration from whitehouse.gov and importing it into
  harvard.edu.