Automatic short answer scoring methods have been developed with various algorithms over the decades. In the Indonesian language, the string-based similarity is more commonly used. This method is difficult to accurately measure the similarity of two sentences with significantly different word lengths. This problem has been handled by the Geometric Average Normalized-Longest Common Subsequence (GAN-LCS) method by eliminating non-contributive words utilizing the Longest Common Subsequence method. However, students’ answers may vary not only in character length but also in the words they choose. For instance, some students tend only to write the abbreviations or acronyms of the phrase instead of writing meaningful words. As a result, it will reduce the intersection character between the reference answer and the student answer. Moreover, it can change the sentence structure even though it has the same meaning by definition. Therefore, this study aims to improve GAN-LCS method performance by incorporating the abbreviation checker to handle the abbreviations or acronyms found in the reference answer or student answer. The dataset used in this study consisted of 10 questions with 1 reference answer for each question and 585 student answers. The experimental results show an improvement in GAN-LCS performance that could run 34.43% faster. Meanwhile, the Root Mean Square Error (RSME) value became lower by 7.65% and the correlation value was increased by 8%. Looking forward, future studies may continue to investigate a method for automatically generate the abbreviations dictionary.