How to align/ justify one reference that has multi-lines

just one reference?  I don’t understand what you mean.  Are they all very short except for the one?  

I assume you are getting “hanging indent” settings.  

There are two places to change this.  Best is in the output style itself in endnote program (edit>output styles, edit your specific style)  see image 1.  But you need to “save as” and then make sure that newly named style is used in your word endnote ribbon.  

You can also change it document to document in word’s endnote ribbon bibliograph layout settings.  see image 2 attached