As process nodes of advanced integrated circuits continue to decrease below 10 nm, the requirement for overlay accuracy is becoming stricter. The alignment sensor measures the position of the alignment mark relative to the wafer; thus, sub-nanometer alignment position accuracy is vital. The Phase Grating Alignment (PGA) method is widely used due to its high precision and stability. However, the alignment error caused by the mark asymmetry is the key obstacle preventing PGA technology from achieving sub-nanometer alignment accuracy. This error can be corrected using many methods, such as process verification and multi-channel weighted methods based on multi-diffraction, multi-wavelength and multi-polarization state alignment sensors. However, the mark asymmetry is unpredictable, complex and difficult to obtain in advance. In this case, the fixed-weight method cannot effectively reduce the alignment error. Therefore, an adaptive weighted method based on the error distribution characteristic of a multi-channel is proposed. Firstly, the simulation result proves that the error distribution characteristic of the multi-alignment result has a strong correlation with the mark asymmetry. Secondly, a concrete method of constructing weight values based on error distribution is described. We assume that the relationship between the weight value of each channel and the deviations of all channels’ results is second-order linear. Finally, without other prior process correction in the simulation experiment, the residual error’s Root Mean Square (RMS) of fixed weighted method is 14.0 nm, while the RMS of the adaptive weighted method is 0.01 nm, when dealing with five typical types of mark asymmetry. The adaptive weighted method exhibits a more stable error correction effect under unpredictable and complicated mark asymmetry.