We study the problem of histogram estimation under user-level differential privacy, where the goal is to preserve the privacy of all entries of any single user. While there is abundant literature on this classical problem under the item-level privacy setup where each user contributes only one data point, little has been known for the user-level counterpart. We consider the heterogeneous scenario where both the quantity and distribution of data can be different for each user. We propose an algorithm based on a clipping strategy that almost achieves a two-approximation with respect to the best clipping threshold in hindsight. This result holds without any distribution assumptions on the data. We also prove that the clipping bias can be significantly reduced when the counts are from non-i.i.d. Poisson distributions and show empirically that our debiasing method provides improvements even without such constraints. Experiments on both real and synthetic datasets verify our theoretical findings and demonstrate the effectiveness of our algorithms.