The clustering ensemble technique aims to combine multiple clusterings into a probably better and more robust clustering and has been receiving an increasing attention in recent years. There are mainly two aspects of limitations in the existing clustering ensemble approaches. Firstly, many approaches lack the ability to weight the base clusterings without access to the original data and can be affected significantly by the low-quality, or even ill clusterings. Secondly, they generally focus on the instance level or cluster level in the ensemble system and fail to integrate multi-granularity cues into a unified model. To address these two limitations, this paper proposes to solve the clustering ensemble problem via crowd agreement estimation and multi-granularity link analysis. We present the normalized crowd agreement index (NCAI) to evaluate the quality of base clusterings in an unsupervised manner and thus weight the base clusterings in accordance with their clustering validity. To explore the relationship between clusters, the source aware connected triple (SACT) similarity is introduced with regard to their common neighbors and the source reliability. Based on NCAI and multi-granularity information collected among base clusterings, clusters, and data instances, we further propose two novel consensus functions, termed weighted evidence accumulation clustering (WEAC) and graph partitioning with multi-granularity link analysis (GP-MGLA) respectively. The experiments are conducted on eight real-world datasets. The experimental results demonstrate the effectiveness and robustness of the proposed methods.