When the lensless Fourier transform digital holography is applied to the microscopic phase-contrast imaging on live cells, the motion of cells will lead to a non-coplanary phenomenon between the object recorded and the reference source. This could result in the imaging aberration. An effective and robust autofocus procedure based on the phase distribution is presented in the paper. With the initial measurement of the distance between the reference source and the hologram, the optimal parameters corresponding to the phase-contrast image can be achieved by a single hologram combined with the linearity fitting. Lensless Fourier transform digital holographic system is built and the experiments on the phase-contrast imaging of the live cervical carcinoma cells are performed. Finally, the good experimental results are obtained. Both the theoretical analysis and the experimental investigation verify the feasibility and the validity of the automatic procedure for non-coplanar aberration compensation.