The way I go about learning languages is that I go through whatever material, learning or otherwise, be it a text or a TV show and then decide which pieces of vocabulary, or sometimes grammar points, that come up will make it into my flashcard app. I'm guessing that by "words to study", you mean something similar to flashcards, where you will revisit the words regularly to help you remember them.
First of all, past a certain point, studying organically, by just ingesting material in your target language, will often become more efficient and fun than doing any kind of formal practice. While I am not more than passingly familiar with Chinese, it seems like you are quite advanced and maybe you should just continue with your reading. Want to make sure those new words you encounter get burned into your mind? Well just read more texts about similar topics. Coming over the same words time and time again, if you can make out the gist of the text and hence infer some of those words, will be a way to fixate those words in your memory.
If you still prefer to do a formal study of some words, then my go-to question for adding words to my flashcards is "Will I encounter this word again?". If the word is related to a topic I am interested in, such as food perhaps, then the answer is "yes", because it is a topic I will read about again. Often times, the answer is "yes" because I've seen the word before, I forgot it's meaning, but I know that I knew it at some point. Sometimes it's "yes" because the word is just plain interesting to me: it could be that the characters that form it form an interesting idea to me or just because I would like to use that word in sentences I compose. When in doubt, add the word anyways. If you came upon it once, then that means it is likely to come up again later.
If that method is too abstract for you, you could try looking the words up in a frequency list and decide upon a cut-off point. Maybe anything beyond the 10,000 most frequent words is not worth adding to your repertoire. A very quick Google search gave me these lists for Mandarin, but there are others: https://en.wiktionary.org/wiki/Appendix:Mandarin_Frequency_lists
You mention that you come upon a lot of words you don't know when read. Don't stop your reading half-way through to look up words you don't immediately know if you can grasp the sentences, just carry on. Once you're done with the text, however, quickly scan it with your eyes for any words that did cause you trouble, you'll even know if they came up multiple times, and note them down. Later on, you can look those words up in a dictionary for their exact meaning or your frequency lists for the relevance.