Deep Neural Network (DNN) testing is one of the most widely-used ways to guarantee the quality of DNNs. However, labeling test inputs to check the correctness of DNN prediction is very costly, which could largely affect the efficiency of DNN testing, even the whole process of DNN development. To relieve the labeling-cost problem, we propose a novel test input prioritization approach (called PRIMA) for DNNs via intelligent mutation analysis in order to label more bug-revealing test inputs earlier for a limited time, which facilitates to improve the efficiency of DNN testing. PRIMA is based on the key insight: a test input that is able to kill many mutated models and produce different prediction results with many mutated inputs, is more likely to reveal DNN bugs, and thus it should be prioritized higher. After obtaining a number of mutation results from a series of our designed model and input mutation rules for each test input, PRIMA further incorporates learning-to-rank (a kind of supervised machine learning to solve ranking problems) to intelligently combine these mutation results for effective test input prioritization. We conducted an extensive study based on 36 popular subjects by carefully considering their diversity from five dimensions (i.e., different domains of test inputs, different DNN tasks, different network structure, different types of test inputs, and different training scenarios). Our experimental results demonstrate the effectiveness of PRIMA, significantly outperforming the state-of-the-art approaches. In particular, we have applied PRIMA to the practical autonomous-vehicle testing in a large motor company, and the results on 4 real-world scene-recognition subjects in autonomous vehicles further confirm the practicability of PRIMA.