The evaluation of neural machine translation systems is usually built upon generated translation of a certain decoding method (e.g., beam search) with evaluation metrics over the generated translation (e.g., BLEU). However, this evaluation framework suffers from high search errors brought by heuristic search algorithms and is limited by its nature of evaluation over one best candidate. In this paper, we propose a novel evaluation protocol, which not only avoids the effect of search errors but provides a system-level evaluation in the perspective of model ranking. In particular, our method is based on our newly proposed exact top-$k$ decoding instead of beam search. Our approach evaluates model errors by the distance between the candidate spaces scored by the references and the model respectively. Extensive experiments on WMT14 English-German demonstrate that bad ranking ability is connected to the well-known beam search curse, and state-of-the-art Transformer models are facing serious ranking errors. By evaluating various model architectures and techniques, we provide several interesting findings. Finally, to effectively approximate the exact search algorithm with same time cost as original beam search, we present a minimum heap augmented beam search algorithm.