Traffic volume is an indispensable ingredient to provide fine-grained information for traffic management and control. However, due to limited deployment of traffic sensors, obtaining full-scale volume information is far from easy. Existing works on this topic primarily focus on improving the overall estimation accuracy of a particular method and ignore the underlying challenges of volume estimation, thereby having inferior performances on some critical tasks. This paper studies two key problems with regard to traffic volume estimation: (1) underdetermined traffic flows caused by undetected movements, and (2) non-equilibrium traffic flows arise from congestion propagation. Here we demonstrate a graph-based deep learning method that can offer a data-driven, model-free and correlation adaptive approach to tackle the above issues and perform accurate network-wide traffic volume estimation. Particularly, in order to quantify the dynamic and nonlinear relationships between traffic speed and volume for the estimation of underdetermined flows, a speed patternadaptive adjacent matrix based on graph attention is developed and integrated into the graph convolution process, to capture non-local correlations between sensors. To measure the impacts of non-equilibrium flows, a temporal masked and clipped attention combined with a gated temporal convolution layer is customized to capture time-asynchronous correlations between upstream and downstream sensors. We then evaluate our model on a real-world highway traffic volume dataset and compare it with several benchmark models. It is demonstrated that the proposed model achieves high estimation accuracy even under 20% sensor coverage rate and outperforms other baselines significantly, especially on underdetermined and non-equilibrium flow locations. Furthermore, comprehensive quantitative model analysis are also carried out to justify the model designs.