Under grid voltage imbalance conditions, the complex interactions among equipment in integrated wind-photovoltaic-energy storage systems significantly increase the risk of electromagnetic oscillations. To suppress negative-sequence voltage and enhance system stability under such conditions, this paper first establishes a linear time-periodic (LTP) model tailored for wind-PV-storage systems. This method fully accounts for time-varying coupling quantities under voltage imbalance, offering higher accuracy compared to classical linear time-invariant (LTI) analysis. Based on the LTP model, the paper comprehensively compares the small-signal stability of the system when grid-connected converters adopt either a positive-sequence single phase-locked loop (PLL) or a positive/negative-sequence dual PLL, guiding the applicable scope of these two control strategies and proposing an adaptive PLL switching control. Furthermore, it investigates the impact of the negative-sequence reactive current coefficient, as specified by national standards for renewable energy grid integration, on the system’s small-signal stability. This study provides guidance for selecting the negative-sequence reactive current coefficient, achieving effective suppression of negative-sequence voltage while ensuring sufficient stability margins.