To implement fine-grained progression signal control on arterial, it is essential to have access to the time-varying distribution of the origin–destination (OD) flow of the arterial. However, due to the sparsity of automatic vehicle identification (AVI) devices and the low penetration of connected vehicles (CVs), it is difficult to directly obtain the distribution pattern of arterial OD flow (i.e., path flow). To solve this problem, this paper develops a semi-supervised arterial path flow estimation method considering the consistency of path flow distribution by combining the sparse AVI data and the low permeability CV data. Firstly, this paper proposes a semi-supervised arterial path flow estimation model based on multi-knowledge graphs. It utilizes graph neural networks to combine some arterial AVI OD flow observation information with CV trajectory information to infer the path flow of AVI unobserved OD pairs. Further, to ensure that the estimation results of the multi-knowledge graph path flow estimation model are consistent with the distribution of path flow in real situations, we introduce a generative adversarial network (GAN) architecture to correct the estimation results. The proposed model is extensively tested based on a real signalized arterial. The results show that the proposed model is still able to achieve reliable estimation results under low connected vehicle penetration and with less observed label data.