Because there are some distinctions in remote sensor characteristics, the methods to abstract information, models for simulation and so on, some differences between the same thematic information may present inevitably. Inter-comparison should be performed before these thematic data being used. Different maps can be compared in a variety of ways. In this paper, the comparison methods are divided into three classes depending on the processed unit, that are comparison based on confusion matrix with pixel unit, comparison based on pattern features with object unit and the others. The advantages and disadvantages of these methods and their corresponding evaluation indexes are stated systematically. Then some uncertainty problems, which are caused by the nature of comparison methods and evaluating indicators, map characteristics, and the scale effect in multi-resolution data, are analyzed. At last, some attentions that should be paid on are presented  for satellite product development teams and product users.