The origin process of manganese ores remains unsolved worldwide. Exploring the origins of stromatolites that contain manganese may be a key to deciphering the sedimentary environments and metallogenic processes of these deposits. However, only a few manganese stromatolites have been discovered and described until now. Microbialites are well developed in the manganese deposits, located near the top of the Ediacaran Doushantuo Formation in Chengkou area of Chongqing, northern Yangtze Craton, but has not been explicitly studied; and whether they are true stromatolites or Epiphyton microbialites remains controversial. Based on field and core observations and thin section microscopy, the characteristics of five types of manganese stromatolites and their growth modes are described in detail in this study. The results show that these stromatolites grew in a biostrome in shoal and lagoon environments and were syngenetic with oncolites and oolites on a carbonate ramp behind the shoal. Manganese stromatolites can be categorized into three forms: (1) stratiform; (2) columnar, which includes branched and columnar types; and (3) stratiform-columnar, which is a transitional type. Based on a criterion that the diameter is less than or greater than 1 mm, columnar stromatolites are further divided into micro-columnar ( 1 mm) columns, which display synchronous growth and are similar to Pseudogymnosolenaceae. Their shapes are mainly controlled by water depths and hydrodynamic strengths. The greater the water depth, the more columnar the columns tend to be. Excessively strong hydrodynamic conditions decrease the growth rate of stromatolites, and they even stopped growth due to wave damage. Furthermore, pillared laminar textures (not Epiphyton), which consist of dendritic, micro-branched and micro-columnar stromatolites, are a common feature of the larger stratiform, stratiform-columnar and columnar stromatolites. The alternations of laminae with different internal textures record subtle fluctuations in water depths and hydrodynamic strengths, which indicate that stromatolite growth is controlled by tidal cycles at the lamina level. Therefore, it is possible that the vertical evolution of the stromatolites could reveal the changing characteristics of both local and regional sedimentary environments, i.e., stromatolite shape changes from columnar to stratiform can represent the onset of shallower environments with weak hydrodynamic conditions. In addition, as important reef builders in shallow carbonate ramps, microstromatolites accelerate the development from ramp to platform. Indicators of microbial control on stromatolite shapes and manganese sedimentation processes include the fabric of stromatolite laminae, organic rhodochrosite with a micritic texture that is usually clotted, spherical, tubular, fibrous or dendritic, which suggests that the laminae resulted from microbially induced in situ precipitation.