This study used a systemic functional linguistic approach to interpret the theme of Lord of the Flies, an allegorical novel written by British writer William Golding. On the basis of the clause, this research analyzed the author’s ways of writing and interpreted the functional meanings he tried to convey through the wording and structure of the novel. Excerptions from Lord of the Flies were analyzed in terms of the three metafunctions of language, namely, ideational function, interpersonal function, and textual function. More specifically, the current study focused on the author’s lexico-grammatical choices in the transitivity system, mood system, and thematic structure of the clauses and revealed that different choices encode different meanings, all contributing to the manifestation of the theme: without proper constraints, human’s inner evil will be magnified indefinitely and their reversion to savagery will be inevitable.