Background: Type-4 clones refer to a pair of code snippets with similar functionality but written in different syntax, which challenges the existing code clone detection techniques. Previous studies, however, highly rely on syntactic structures and textual tokens, which cannot precisely represent the semantic information of code and might introduce nonnegligible noise into the detection models. Aims: To overcome these limitations, we explore an effective semantic-based solution for Type-4 clone detection. Additionally, we conducted an empirical study on the characteristics of Type-4 clone pairs. We found that NOT all tokens contain semantics that the Type-4 clone detection required. Operators and API calls emerge as distinct candidates for Type-4 code semantic representation. Method: To bridge this gap, we design a novel semantic graph based deep detection approach, called SEED. For a pair of code snippets, SEED constructs a semantic graph of each code snippet based on intermediate representation to represent the code functionality more precisely compared to the representations based on lexical and syntactic analysis. To accommodate the characteristics of Type-4 clones, a semantic graph is constructed focusing on the operators and API calls instead of all tokens. Then, SEED generates the feature vectors by using the graph deep neural network and performs code clone detection based on the similarity among the vectors. Results: Extensive experiments show that our approach significantly outperforms two baseline approaches over