Complex fracture networks (CFN) provide flow channels and significantly affect well performance in unconventional reservoirs. However, traditional rate transient analysis (RTA) models barely consider the effect of CFN on production performance. The impact of multi-phase flow on rate transient behaviors is still unclear especially under CFN. Neglecting these effects could cause incorrect rate transient response and erroneous estimation of well and fracture parameters. This paper investigates multi-phase rate transient behaviors considering CFN and tries to investigate in what situations the multi-phase models should be used to obtain more accurate results. First, an embedded discrete fracture model (EDFM) is generated instead of Local Grid Refinement method to overcome time-intensive computation. The model is coupled with reservoir models using non-neighboring connections (NNCs). Second, eight cases are designed using the EDFM technology to analyze effect of natural fractures, formation permeability, and relative permeability on rate transient behaviors. Third, Blasingame plot, log–log plot, and linear flow plot are used to analyze the differences of rate transient response between single-phase and multi-phase flow in reservoirs with CFN. For multi-phase flow, severe deviations can be observed on RTA plots compared with single-phase model. Combination of three RTA type curves can characterize the differences from early to late flow regimes and improve the interpretation accuracy as well as reduce the non-unicity. Finally, field data analysis in Permian Basin demonstrates that multi-phase RTA analysis are required for analyzing production and pressure data since single-phase RTA analysis will lead to big errors especially under high water cut during fracturing fluid flowback period, early production of unconventional gas wells or after waterflooding, or water huff-n-puff.