Vehicle–road–cloud integrated systems have great potential in terms of improving traffic efficiency and achieving intelligent automatic driving through the integration of on–board terminals, roadside facilities, and cloud computing. However, their operational capabilities are heavily reliant on ultra-low-latency collaborative communication. This paper constructs a latency fault tree model to comprehensively analyze multi-source triggering paths of computation delay and reveals the formation mechanism of the delay path from “germination–induction–evolution”. On this basis, the Analytic Hierarchy Process is used to construct a three-level evaluation framework, and the influencing factors are quantitatively evaluated using NS-3 simulation data of the 004-V2X Communication Performance Testing Dataset. The result shows that the weight value of the network communication layer is the largest, 0.498, which shows that the bottleneck of performance in network communication is the wireless link quality. The cloud processing layer is second 0.327, which is dominated by the computational complexity and resource allocation policy. The impact of the onboard terminal layer is the smallest, 0.175. The FTA–AHP framework supported by empirical data can find the key factors affecting delay, which can help engineering optimization. It is noted that the AHP consistency check (CR) just checks the inner transitivity of expert judgment (i.e., the matrix consistency), while it cannot assure the objectivity and the bias elimination. We reduce the subjectivity by combining multiple experts, anchoring judgment with the simulation data, and performing a sensitivity check on the perturbation of the weights.