This paper is concerned with the generalization analysis on learning to rank for information retrieval (IR). In IR, data are hierarchically organized, i.e., consisting of queries and documents per query. Previous generalization analysis for ranking, however, has not fully considered this structure, and cannot explain how the simultaneous change of query number and document number in the training data will affect the performance of algorithms. In this paper, we propose performing generalization analysis under the assumption of two-layer sampling, i.e., the i.i.d. sampling of queries and the conditional i.i.d sampling of documents per query. Such a sampling can better describe the generation mechanism of real data, and the corresponding generalization analysis can better explain the real behaviors of learning to rank algorithms. However, it is challenging to perform such analysis, because the documents associated with different queries are not identically distributed, and the documents associated with the same query become no longer independent if represented by features extracted from the matching between document and query. To tackle the challenge, we decompose the generalization error according to the two layers, and make use of the new concept of two-layer Rademacher average. The generalization bounds we obtained are quite intuitive and are in accordance with previous empirical studies on the performance of ranking algorithms.