As a researcher in a pharmaceutical company with a PhD in Biology and H1B status, I want to apply for Green Card in EB1 or NIW, or apply for 2 categories at the same time. It is very difficult for me to get reference letters form US government agencies or some professional societies. Do I have to get reference letters for those applications? and are there any thing more I should know more about the reference letters?

There are many issues to be addressed about reference letters. First, the reference letters are not required by USCIS. But, they can be very useful, and most USCIS examiners for EB1 and NIW application expect them. 

Some applicants may try to avoid the reference letters for confidentiality purposes, but for others, they are easy to obtain. A more thorough compilation of background materials can offset an absence of reference letters. These materials may include statistics about the area of research, information about professional organizations, awards, journals, etc. 

Some professional societies usually do not provide reference letters of their members. In addition, government agencies will not simply prepare a reference letter if asked. So the request of reference letters or “independent letters” heavily favors applicants with connections at government agencies or in professional societies, which may see as unfair for some applicants.