As network simulator has been suffering from the large computational complexity in the physical (PHY) layer, a PHY layer abstraction model that efficiently and accurately characterizes the PHY layer performance from the system level simulations is well-needed. However, most existing work investigate the PHY layer abstraction under an assumption of perfect channel estimation, as a result, such a model may become unreliable if there exists channel estimation error in a real communication system. This work improves an efficient PHY layer method, EESM-log-SGN PHY layer abstraction, by considering the presence of channel estimation error. We develop two methods for implementing the EESM-log-SGN PHY abstraction under imperfect channel estimation. Meanwhile, we present the derivation of effective Signal-to-Interference-plus-Noise-Ratio (SINR) for minimum mean squared error (MMSE) receivers impacted by the channel estimation error. Via full PHY simulations, we verify that the effective SINR is not impacted by the channel estimation error under multiple-input and single-output (MISO)/single-input and single-output (SISO) configuration. Finally, the developed methods are validated under different orthogonal frequency division multiplexing (OFDM) scenarios.