Abstract: Pipeline transport loss is an important economic index for natural gas transmission and distribution business and also an economic parameter greatly concerned at both sides of custody transfer. This paper analyzes how the errors in resolution of the metering system and in calculation of pipe inventory and blow-down volume on the transport loss, and clearly puts forward that the error of the metering system is the primary cause for transport loss of gas trunk line. The uncertainty analysis model of the complex flow metering system for gas trunk line is established. Based on the error synthesis and transfer theory, total uncertainties at both inlet and outlet of the pipeline system are obtained. A calculation method of pipeline transport loss index is proposed. The application shows that the index comparison of actual loss and loss can be used for warning of pipeline loss, in order to provide a reference for the repair and replacement of flowmeter.