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Third-party libraries with rich functionalities facilitate the fast development of Node.js software, but also bring new security threats that vulnerabilities could be introduced through dependencies. In particular, the threats could be excessively amplified by transitive dependencies. Existing research either considers direct dependencies or reasoning transitive dependencies based on reachability analysis, which neglects the NPM-specific dependency resolution rules, resulting in wrongly resolved dependencies. Consequently, further fine-grained analysis, such as vulnerability propagation and their evolution in dependencies, cannot be carried out precisely at a large scale, as well as deriving ecosystem-wide solutions for vulnerabilities in dependencies. To fill this gap, we propose a knowledge graph-based dependency resolution, which resolves the dependency relations of dependencies as trees (i.e., dependency trees), and investigates the security threats from vulnerabilities in dependency trees at a large scale. We first construct a complete dependency-vulnerability knowledge graph (DVGraph) that captures the whole NPM ecosystem (over 10 million library versions and 60 million well-resolved dependency relations). Based on it, we propose DTResolver to statically and precisely resolve dependency trees, as well as transitive vulnerability propagation paths, by considering the official dependency resolution rules. Based on that, we carry out an ecosystem-wide empirical study on vulnerability propagation and its evolution in dependency trees. Our study unveils lots of useful findings, and we further discuss the lessons learned and solutions for different stakeholders to mitigate the vulnerability impact in NPM. For example, we implement a dependency tree based vulnerability remediation method (DTReme) for NPM packages, and receive much better performance than the official tool (npm audit fix).