It is the most important unconformity among the numerous unconformities may causing Karst reservoir in Tarim Basin that was developed between the Middle and Upper Ordovician. Based on the structural characteristics of the unconformity in Tazhong uplift, the origin mechanisms of the unconformity are analyzed. Studies show that crustal-scale folding controlls the development of the unconformity between the Middle and Upper Ordovician during Qiaerbake deposition period, and the unconformity distribution is controlled by anticline zone. All the stratigraphic hiatus in the anticlinal zone is not caused by denudation, in which only the hiatus in Yingshan and Yijianfang Formations were caused by denudation, but the hiatus was caused by without deposition in Qiaerbake Formation showing differences reasons in resulting the stratigraphic hiatus. It can be divided the unconformity between the Middle and Upper Ordovician into two types, that are syn-tectonicunconformity and post-tectonic unconformity. The syn-tectonicunconformity was developed between Qiaerbake Formation and Yijianfang Formation distributing in the limb of Tazhong anticlinal uplift. The post-tectonic unconformity was developed between Lianglitage Formation and Yingshan Formation distributing in the top of Tazhong anticlinal uplift.