Adaptive proportional resonant (PR) controllers, whose resonant frequencies are obtained by the phase-locked loop (PLL), are employed in grid connected voltage source converters (VSCs) to improve the control performance in the case of grid frequency variations. The resonant frequencies can be estimated by either synchronous reference frame PLL (SRF-PLL) or dual second order generalized integrator frequency locked loop (DSOGI-FLL), and there are three different implementations of the PR controllers based on two integrators. Hence, in this paper, system stabilities of the VSC with different implementations of PR controllers and different PLLs under weak grid conditions are analyzed and compared by applying the impedance-based method. First, the αβ-domain admittance matrixes of the VSC are derived using the harmonic linearization method. Then, the admittance matrixes are compared with each other, and the influences of their differences on system stability are revealed. It is demonstrated that if DSOGI-FLL is used, stabilities of the VSC with different implementations of the PR controllers are similar. Moreover, the VSC using a DSOGI-FLL is more stable than that using a SRF-PLL. The simulation and experimental results are conducted to verify the correctness of theoretical analysis.