This paper addressed the problem of highway traffic flow multivariate time series forecasting with the challenges of variate heterogeneity. To improve forecast performance without a heavy computational burden in large-scale networks, we innovatively introduced variational mode decomposition and established a decomposition-assisted multi-tasking deep learning forecasting architecture. To improve variate-specific pattern learning and mitigate pattern mixing, we proposed a novel temporal-frequency pure convolutional neural network incorporating discrete Fourier transform, deepwise convolution, and batchwise feedforward neural network. To verify the proposed model, we conducted a case study on a regional network located in Jiangsu, China. Results demonstrate strong forecast performance and efficient computation. The proposed model offers suitability toward highway operators for large-scale engineering deployment and better facilitates their managerial actions.