The measurement of short pulse X-ray of high energy produced by Qiangguang Ⅰ accelerator for radiation effect study includes X-ray dose and pulse duration measuring. The thermoluminescence dosemeter (TLD) is used to measure X-ray dose, and the PIN semiconductor detector is employed for recording waveforms of X-ray. The dose rate is calculated out by the results of X-ray dose and pulse duration. By the mathematic model of uncertainty, factors with important effect on X-ray measuring are analyzed. For the measurement uncertainty of X-ray pulse duration is 3.7%, the measuring of X-ray dose with relative standard uncertainty of 25.1% plays a crucial role in determining X-ray dose rate, and the expanded uncertainty of dose rate is about 50.8% with confidence probability of 95%.