The overall performance and emission during a speed/torque versus time transient cycle are investigated in a heavy-duty truck engine equipped with an intake valve closing timing mechanism and a two-stage turbocharger system (high-pressure turbine is variable geometry turbine). The performance discrepancy analysis between steady-state and transient operation is completed based on a fairly optimized steady-state baseline. The result shows that during the transient operation, the transient NOx emission can track the steady-state baselines much better than particle matter, and the cumulative NOx in transients is even lower than the cumulative NOx of the steady-state baselines, while the rising particle matter emissions mainly due to appearance in particle matter emission spikes during the cycle. And the transient particle matter spikes appeared almost in two typical transient conditions: sharp acceleration from idling and abrupt load transients. The instantaneous equivalence ratio (F) is found to be the main physical factor governing particle matter spikes formation in transients. Particle matter spikes become prominent when F cannot track the steady-state baseline well or F rises over a critical value of 0.8. The control strategy of intake valve closing timing mechanism-variable geometry turbine-exhaust gas recirculation to bridge the gap of F between the steady-state and the transients has been established, which effectively cut down the emission spikes, reducing particle matter emissions by 32.9% with almost no change in NOx.