Micro-Electro-Mechanical System (MEMS) based Strapdown Inertial Navigation System (SINS) is preferred for pipeline surveying as it has several priorities including low-cost, small-size, light-weight, and low-power consumption. It acts as a significant tool for localization on potential pipeline defects in pipeline inspection and repair missions. Moreover, it provides measurements to calculate the pipeline centerline coordinates and the horizontal and vertical pipeline curvatures. However, its precision degrades significantly in small diameter pipeline surveying application with both continuous 3D velocity updates and discrete coordinate updates. Attitude updates are an enhanced technique for SINS errors correction in pipeline surveying system. The azimuth and pitch angles of Pipeline Inspection Gauge (PIG) are constant within each straight pipeline segments. This paper introduces a novel pipeline junction detection method by analyzing low-cost MEMS accelerometer measurement data using Fast Orthogonal Search (FOS). The simulated pipeline surveying data sets are obtained in a laboratory environment by Inertial Measurement Unit (IMU), which is mounted on three-axis positioning and rate table. The accelerometer measurement data are extracted and analyzed by FOS. The detection result demonstrated that FOS can detect the pipeline junction with accelerometer measurement data successfully. The FOS pipeline junction detection result provided accurate indication for azimuth and pitch angles measurement updates in SINS at each straight pipeline segment. Moreover, the detection result is expected to provide significant improvement for the MEMS SINS pipeline surveying system precision with reduced cost.