A phase-locked loop (PLL) with novel phase detection mechanism is provided, including a phase frequency detector (PFD), a controller, a digital-to-analog (D2A) module, and a voltage-controlled oscillator/current-controlled oscillator (VCO/ICO), wherein PFD has a reference signal input and an input from the output signal of the VCO/ICO and is connected to the controller, the controller is then further connected to the D2A module, the D2A module converts the control signal from the controller into an analog voltage to control the frequency and phase of VCO/ICO. It is worth noting that the PFD of the present invention has a novel phase detection mechanism so that the phase detection can be accomplished by observing signal level transitions of the reference signal input and a delayed reference signal with respect to the output signal of the VCO/ICO without edge alignment. In addition, the novel phase detection mechanism also allows flexible reference signal input.