This paper proposes mining query subtopics from questions in community question answering (CQA). The subtopics are represented as a number of clusters of questions with keywords summarizing the clusters. The task is unique in that the subtopics from questions can not only facilitate user browsing in CQA search, but also describe aspects of queries from a question-answering perspective. The challenges of the task include how to group semantically similar questions and how to find keywords capable of summarizing the clusters. We formulate the subtopic mining task as a non-negative matrix factorization (NMF) problem and further extend the model of NMF to incorporate question similarity estimated from metadata of CQA into learning. Compared with existing methods, our method can jointly optimize question clustering and keyword extraction and encourage the former task to enhance the latter. Experimental results on large scale real world CQA datasets show that the proposed method significantly outperforms the existing methods in terms of keyword extraction, while achieving a comparable performance to the state-of-the-art methods for question clustering.