According to the copious research conducted on emergency ventilation in tunnel during fire, when plug-holing and boundary layer separation occur, the actual smoke extraction efficiency is unable to satisfy the emergency ventilation design criteria in tunnels. By and large, so necessary and precious is it that a novel method would be presented in order to improve smoke extraction efficiency of ventilation systems with vertical mid-tunnel shafts to provide visibility and possibility of scape for passengers, and rescue services. This research has been carried out to investigate the simultaneous effects that adding a board-coupled shaft and using a bevel-angle connection between shaft and ceiling could have on plug-holing and boundary layer separation. Placing a slim board beneath the shaft and substituting the right-angle with a bevel-angle connection, extremely attenuated the negative effects of the aforementioned phenomena and led to higher smoke extraction efficiency. Mass flow rate of smoke through the outlet of the mid-tunnel shaft was compared numerically for different board gaps, sizes and connection angles using fire dynamic simulator. The results have good agreement with the experimental data in literature. Furthermore, the mentioned changes in the mid-tunnel shaft lead to higher mass flow rates, which is to approximately two times higher smoke extraction efficiency than those in the previous studies. Ultimately, through the prediction model, which is performed through numerical simulation data and machine learning algorithm called neural network, the optimal values of the connection angle, dimensionless area and gap range from 65° to 68°, 5.4 to 9.6 and 0.7 to 0.85, respectively.