The invention discloses a fault root cause positioning method for a micro-service system, which comprises the following steps of: acquiring call chain data in the micro-service system in real time, converting the call chain data into four business indexes and monitoring in real time, when an exception is found, constructing a service topological graph, a process topological graph and a host topological graph by using a call chain in an exception time period, calculating an abnormal score of each node on the topological graph, and finally positioning to a root cause node, namely a process node or a host node, according to a sequence from large depth to small depth and from process to host. According to the obtained call chain data, the topological relation of the host level can be dynamically constructed, the topological relation of the process level and the topological relation of the service level can also be dynamically constructed, and data guarantee is provided for more accurate root cause positioning. According to the method, the call chain data in the abnormal time period are analyzed in real time by utilizing an unsupervised algorithm, and training data and labels are not needed.