In this paper, an autonomous subnet based structural methodology for bottom-up synthesis of Petri Nets for Flexible Manufacturing Systems is proposed. Furthermore, the theoretical analysis of the model constructed by the method is carried by intensively using model's structural information, such as invariants, siphons, etc.. As a result, the analysis leads us to draw the general conclusion that the model obtained is conservativeness and thus bound, and characterize its liveness in terms of zero-marking minimal siphons. It is based on model's structural information that distinguishes our method from others. In line of this thought, a liveness guarantying policy for the obtained model is proposed. Some control subnets are merged into the original model according to the proposed synthesis rules in this paper to ensure that no minimal siphons are emptied in any state, therefore the liveness is guaranteed. As a result, a live, conservative and revertible Petri Nets is obtained. A practical example is also presented to demonstrate the effectiveness of this method.