For the most part, as long as the recommendation is strong this will not be an issue. Your reliability as an intellectual in the Intelligence Community is a function of your personal characteristics not the nationality of the people writing your Letters of Recommendation. While it is true that substantial affiliation with foreign nationals can raise questions, they are not necessarily obstacles to clearances, so long as your other bona fides are in order (e.g. finances, drug use).
Depending on the area of intelligence, an Letter of Recommendation from a Chinese national may actually help you. If you are an expert on China, or are hoping to work on China as a thematic interest, showing that you have ties to China is no bad thing. Even in the security clearance process, you will need to reveal this association, and doing so up front is only to your benefit.
Far more important is the content of the Letter of Recommendation, and the nature of the relationship. While not a part of your question, these kinds of Letters of Recommendation should be very similar in character to other academic letters. If this recommender would not be your Letter of Recommendation writer for other jobs, I would not make him the writer for this job, either. You want people who know you and your work well, because they will be able to write the best Letters of Recommendation, regardless of national background.
On a side note, while it won't hurt you if your Letter of Recommendation writer is Chinese, if s/he is an American citizen it cannot hurt for them to say so in the letter. It changes the dynamic of the background investigation, just a little.