Charge transfer efficiency (CTE) is a very important characteristic parameter for the CCD in the scientific imaging applications, especially in the imaging systems used to observe very faint objects such as night astronomical cameras. Several popular CTE measurement techniques are introduced briefly in this paper, deficiencies in the techniques are pointed out, and then some improvements are made. The modified algorithm for CTE measurement is based on the x-ray transfer and the MATLAB. When the algorithm begins, an appropriate initial charge transfer line from the x-ray single-pixel-events plot and its interzone for computation are determined by the user-PC interaction, and then a linear fit is performed in the interzone so as to get a more accurate transfer line. Thus a new interzone is obtained and a next linear fit can be done. In this way, a more accurate value of CTE can be obtained. Usually the algorithm stops after 5 to 10 iteration steps. Moreover the accuracy of the algorithm is discussed. Finally, the algorithm is used to estimate the horizontal CTE for 2 KAF-4301E CCDs tested at low temperatures. The results indicate that, when the CCD operating temperature is reduced below its absolute minimum rating, although the dark current performance improves obviously, the CTE performance degrades rapidly. An analysis and discussion for the results at the depth of theory is presented.