The pseudolite system, an alternative to global navigation satellite systems, can provide centimeter-level positioning accuracy using carrier phase measurements. The carrier phase-based positioning accuracy is determined by the tracking performance of the phase-locked loop (PLL), since cycle slip may cause carrier phase measurement bias. To overcome the near-far problem, the pulsing scheme is often adopted in pseudolite positioning systems. For the pulsed pseudolite signal, the carrier tracking loop is more prone to cycle slip compared to the conventional continuous signal. For improving the performance of the PLL tracking the pulsed pseudolite signal at low carrier-to-noise ratios, a PLL with multi-pulse coherent integration (MPCI-PLL) is proposed. The thermal noise performance of the digital PLL (DPLL) is determined by its equivalent noise bandwidth. When the product of the design noise bandwidth and the loop update interval increases, the true equivalent noise bandwidth of DPLL tends to be larger than the design value. Then, the closed-form expression of the single-sided equivalent noise bandwidth of first-, second-, and third-order DPLL is derived by the discrete frequency domain approach. The proposed MPCI-PLL is tested in both simulations and a real experiment. Compared to the conventional method of tracking the pulsed pseudolite signal, the proposed carrier tracking loop significantly decreases the probability of a cycle slip at low signal-to-noise ratios. Simulation and experimental results show that the improvement is about 3–4 dB.