For a language pair such as Chinese and Korean that belong to entirely different language families in terms of typology and genealogy, finding the correspondences is quite obscure in word alignment. We present annotation guidelines for Chinese-Korean word alignment through contrastive analysis of morpho-syntactic encodings. We discuss the differences in verbal systems that cause most of linking obscurities in annotation process. Systematic comparison of verbal systems is conducted by analyzing morpho-syntactic encodings. The viewpoint of grammatical category allows us to define consistent and systematic instructions for linguistically distant languages such as Chinese and Korean. The scope of our guidelines is limited to the alignment between Chinese and Korean, but the instruction methods exemplified in this paper are also applicable in developing systematic and comprehensible alignment guidelines for other languages having such different linguistic phenomena.