Objectives: The previous researches have different recognitions and debates in understanding the interposition relationship and internal sequences of the Shangxi Group and the Likou Group within the Neoproterozoic basement from the adjacent area among Anhui—Zhejiang—Jiangxi Provinces. The field geological phenomenas and former study results show that there is a significant difference in metamorphic and deformation characteristics of the Neoproterozoic basements between the north and south sides of the Shexian—Qimen fault. Methods: By observing the sequence sections and key spots like reverse unconformable interface between the Nanhua and Neoproterozoic basement from Sanyang Town, Shexian County, and the intrusion relation between the Shangxi group and the Xucun pluton from Chenkan Town, as well as combining with the published age data, this paper believed that the lowest bed of the Neoproterozoic basement is the Niuwu Formation, the Likou group should be placed above the Shangxi group. Results: The field geological phenomenas from Qiashe—Zhaixi section, Hongguan—Banqiao—Xikou section and other scattered points, associated with some petrographic analysis and existing data, show that the upper and lower strata of the Neoproterozoic basements in the north of the fault zone are not metamorphic or shallow metamorphic (belongs to stratified and ordered rock series). But in the south, the Neoproterozoic strata are characterized by medium metamorphic and strong deformation (belongs to flaky and disordered rock series). Conclusins: This deformation occurred during the Caledonian tectonic events according to the published deformation ages. Caledonian tectonic event caused the difference of the metamorphic and deformation characteristics of the Neoproterozoic basements between the north and south sides in the adjacent region among Anhui, Zhejiang, and Jiangxi Provinces. The reason was that the Caledonian orogenic event in the south China had extended and resulted in regional metamorphism and corresponding deformation in the northwest of Jiangshan—Shaoxing orogenic belt. However, the dynamical stress was weakened in the north of the Shexian—Qimen fault zone because of the northward thrust along the Shexian—Qimen fault zone and uprising—erosion in the south, which leading to the weak deformation environment in the north side of the Shexian—Qimen fault zone than that of the south.