The autoregressive sieve (ARS) bootstrap method can capture the correlation of time series and expand the original data set to the required volume. In this study, we introduce the ARS bootstrap into the matrix constant false alarm rate (CFAR) method to counter the inability of the Monte Carlo methods to extract the detection threshold due to the limited number of pulses under a certain false alarm probability. We assume the echo data of each range cell in a coherent processing interval (CPI) to be a stationary time series, and regard target detection as a two-sample hypothesis testing problem. We propose a statistic to test the equivalence of the autocovariance corresponding to two potential time series by using the correlation between pulses in a short pulse dataset, and analyze the validity of the ARS bootstrap for this statistic. The statistic distribution is obtained according to the bootstrap procedure and the threshold is obtained under fixed false alarm probabilities. Numerical experiments on the simulated and real sea clutter data were conducted to compare the detection results of the partial matrix CFAR detectors for the short and long pulse cases. With the introduction of the bootstrap method, we do not need to model the clutter amplitude distribution and the related statistical characteristics during target detection. To improve the detection probability with low signal-to-clutter ratio (SCR), we propose the two-sample autocovariance vector (ACV) detector based on the proposed statistic and use the correlation properties between pulses. We observed a 28% increase in detection probability when the SCR was 0 dB compared to other matrix CFAR methods, such as detectors based on Logarithmic Euclidean (LE) distance, Kernel Function-based Symmetric Kullback-Leibler (KSKL) divergence, and Total Bregman divergence (TBD) for the short pulse case.