The phosphine-catalyzed [4 + 2] annulations between allenoates and electron-poor trifluoromethyl ketones or N-tosylbenzaldimine dipolarophiles have been investigated in continuum solvation using density functional theory (DFT) calculations. The detailed reaction mechanisms as well as the high cis-diastereoselectivities of the reactions have been firstly clarified. Our calculated results reveal that the whole catalytic process is presumably initiated with the nucleophilic attack of phosphine catalyst at the allenoate to produce the zwitterionic intermediate M1, which subsequently undergoes γ-addition to the electron-poor CO (or CN) dipolarophile to form another intermediate M2. The following [1,3] hydrogen shift of M2 is demonstrated to proceed via two consecutive proton transfer steps without the assistance of protic solvent: the anionic O6 (or N6) of M2 first acts as a base catalyst to abstract a proton from C1 to produce the intermediate M3, and then the OH (or NH) group can donate the acidic proton to C3 to complete the [1,3] hydrogen shift and generate the intermediate M4. Finally, the intramolecular Michael-type addition followed by the elimination of catalyst furnishes the final product. High cis-diastereoselectivities are also predicted for both the two reactions, which is in good agreement with the experimental observations. For the reaction of allenoates with trifluoromethyl ketones, the first proton transfer is found to be the diastereoselectivity-determining step. The cumulative effects of the steric repulsion, electrostatic interaction as well as other weak interactions appear to contribute to the relative energies of transition states leading to the diastereomeric products. On the contrary, in the case of N-tosylbenzaldimines, the Michael-type addition is found to be the diastereoselectivity-determining step. Similarly, steric repulsion, as well as electrostatic interaction is also identified to be the dominant factors in controlling the high cis-diastereoselectivity of this reaction.