The void defect evolvement and molecular conformational transition in crystalline δ-HMX were simulated applying molecular dynamics (MD) method and a compared research with β phase was performed. The simulated system contains a void defect with size of 30 HMX molecules, corresponding to 10% concentration of vacancies. The energy barriers for molecular conformation conversions in vacuum were calculated by the QST3 method. Results show that all the conformation transitions have low activation energy. At the simulation temperature of 500 K, whether the δ phase or β phase, the whole crystal completely collapses into liquid state and is accompanied by a large lattice expansion. In the collapsed liquid molecules, four kinds of molecular conformations, α, β, BB(boat-boat) and BC(boat-chair), can be observed. A large number of transition states and intermediate structures coexist with four kinds of molecular conformations. Tracing the evolvement of single molecule with time during MD simulation can find the frequent transition between different conformations due to low conversion energy barriers. When simulated temperature decreases to 300 K and 200 K, two crystalline phases present different evolvement trends. For δ-HMX system, the void collapse occurs and the whole lattice loses strict periodic structure, but the void inserted into β-HMX is still hold on and there only occur the shrink of void and shift of a few molecules toward the center of void. In addition, in contrary to the lattice shrink of δ-HMX, the volume of β-HMX continuously expands with rising the simulated temperature.