Pedagogical agents (PAs) are a crucial aspect of the e-learning environment. A PA is defined as a virtual character presented on an interface, and they are designed to promote student learning. PAs have been widely discussed in academic papers. However, an appropriate analysis framework has not been proposed because of the diversity and complexity of PAs. Therefore, we reviewed the literature and proposed a list of related clues, including environmental, learner, role, appearance, and social clues. We used this framework to analyse the learning effectiveness of PAs in specific areas. The keyword 'pedagogical agent' was used to search for related papers from 2000 to 2019. A total of 136 related papers were obtained. A meta-analysis was performed using a random effects model (Hedges' g was used to measure the effect size). The effect size of the learning effectiveness of PA was small to medium (g = 0.423). The results of subgroup analysis (Hedges's g) revealed that subjects, grades, additional support, appearance style, and facial expression changes had a different moderating effect on the effect of PA on learning effectiveness. We discussed the moderating effect of related clues and suggested future research directions.