If you have a tendency to use a certain word or phrase very frequently, you can come across as a more eloquent writer or speaker, and your writing can flow better, if you actively try to limit your use of that word or term.
But this applies to English/language in general and I wouldn't worry about this when writing a research paper any more than I usually do (but I'm usually semi-formal and fairly pedantic about my use of language). The goal of a research paper is to clearly convey the methods, data and results of some research. Eloquence and well-flowing text is easier and more pleasant to read, which is helpful, but this is secondary to clarity (it doesn't help to have a paper with text that's easy to read, but where the actual research isn't understood or it's misunderstood).
Using synonyms is one way to avoid the overuse of certain words, but, like others have mentioned, you can't necessarily do this in a technical research paper. It can cause confusion to use different terms for the same thing and often it would be more clear to just stick to the same word. If you were replacing e.g. "likely" with "probably", that's much less likely to cause an issue, given that different instances of those words are typically not so closely linked (although they do mean slightly different things).
Rephrasing is another way to avoid word overuse. You could possibly avoid reusing a word by combining sentences. Although long sentences tend to be more confusing, so try not to overdo it.
Using pronouns like "it", "this", "them", etc. is also a common technique to avoid word reuse. Although this may also lead to more confusing sentences, as it's not always clear which noun a pronoun is referring to, so approach with caution.
As an example, this would sound very unnatural (not only due to the repetition of "equation"):
The equation is based Newton's laws. The equation was determined in consultation with leading experts. But no-one fully understands why the equation works.
It can be rephrased to something like the below, which sounds much better.
The equation is based Newton's laws and was determined in consultation with leading experts. But no-one fully understands why it works.
But you'll need to figure out how to do this (if it's even possible or a good idea) largely on a case-by-case basis.