To improve the beam performance of the two-bunch acceleration (two macro beam pulses in one macro microwave pulse), a new sub-harmonic bunching system has been designed and optimized for BEPCII Linac. Due to the difference between the new bunching system and the present one, the physical tolerances to the key components must be reconsidered. In this paper, the most important jitter effects in the new bunching system are studied systematically, which include the gun timing,high voltage jitters, the phase and power jitters of the two sub-harmonic bunchers and the phase jitters of the 4-cell traveling wave buncher and A0(accelerating section in the bunching system) accelerating tube. A multi-particle simulation program PARMELA is employed, and the physical tolerances of the jitters have been