In vector tracking loop (VTL), the relativity among received signals is exploited to deeply integrate the entire information within signal processing channels. However, the tracking error in one channel may corrupt other channels and lead to an increasing degradation in the tracking performance. An adaptive GPS vector tracking loop with the detection and isolation of contaminated channels is proposed to suppress the propagation of tracking error and to make the vector-based receiver less vulnerable in poor signal quality environments resulting from signal attenuation, interference and jamming. The vectorial transfer function models and the noise bandwidths of both the vector frequency lock loop and the vector delay lock loop are established to accurately calculate bandwidths and optimally design parameters for VTL is superior to baseline VTL, allowing the accuracy, the availability and the reliability of the vector-based receiver to be improved. In conclusion, the proposed adaptive VTL with the detection and isolation of contaminated channels is a powerful method for applications in GPS-challenged environments.