This paper is the first to demonstrate and simulated a simple and systematic transfer matrix (T-matrix) method for analyzing the accumulated effects of Rayleigh Backscattering (RB) and Fresnal reflection (FR) crosstalk on signal transmission in bidirectional single-fiber WDM-PON systems for the conventional (usually 20 km transmission without any amplification in remote node) and comparing with the analytical methods. Secondly by using analytical method we are going to analyse the three cases for long-reach WDM-PONs (100km by utilizing optical amplifier to enhance the power budget) in the first case the best crosstalk-to-signal (C/S) is achieved when the Remote Node (RN) is placed either near to the Central office (CO) or Optical Network Unit (ONU) section. And in the second case, we are going to achieve the best effective crosstalk-to-signal (C/S) ratio when the Remote Node (RN) gain is placed at the middle of transmission link. And in the third case, the crosstalk-to-signal (C/S) ratio gets worse nearly by 1.5 dB in the presence of a strong reflection (r = 30 dB). Eventually if the FR is increased by the smaller reflectivity and therefore EDFA gain must be exaggerated, the crosstalk-to-signal (C/S) ratio will even get worse when EDFA is placed near to ONU section. This happens due to the reamplification and re-modulation feedbacks of back reflections that may occur in the Transmission of the signal at Remote Node (RN). This transfer matrix method is efficient, powerful (when comparing with the analytical methods). Its accuracy is verified for straight forward system architectures and then applied for complex architectures of long-reach hybrid WDM-PONs. © 2006-2017 Asian Research Publishing Network (ARPN).