Effects of protein denaturation caused by high pressure freezing, involving Pressure-Factors (pressure, time) and Freezing-Factors (temperature, phase transition, recrystallization, ice crystal types), are complicated. In the current study, the conformation and functional changes of natural actomyosin (NAM) under pressure assisted freezing (PAF, 100,150,300,400,500 MPaP−20 °C/25 min), pressure shift freezing (PSF, 200 MPaP−20 °C/25 min), and immersion freezing (0.1MPaP−20 °C/5 min) after pressure was released to 0.1 MPa, as compared to normal immersion freezing process (IF, 0.1 MPaP−20 °C/30 min). Results indicated that PSF (200 MPaP−20 °C/30 min) could reduce the denaturation of frozen NAM and a pressure of 300 MPa was the critical point to induce such a denaturation. During the periods of B → D in PSF or B → C → D in PAF, the generation and growth of ice crystals played an important role on changing the secondary and tertiary structure of the treated NAM.