Abstract: For short burst communication systems, the position and the number of pilot symbols have a great impact on frequency estimation accuracy and estimation range in time-domain correlation frequency estimation algorithm. So a frequency estimation algorithm with a high frequency estimation accuracy based on the summation of the entire cross correlation is proposed, and its theoretical estimation variance is derived. By analyzing the impact of the pilot position on estimation accuracy and estimation range, a scheme of Variable D-spaced Preamble Middle (VDPM) frame structure is proposed which can choose the distance of pilot blocks according to estimation accuracy and estimation range. Theoretical analysis and simulation results show that the frame structure can satisfy the requirements of frequency estimation range and estimation accuracy, and the estimation algorithm can achieve high estimation accuracy with a few pilot symbols, hence it is suit for short burst communication system.