The hydrogen bonding interactions between ureas or thioureas and different nitro-compounds were studied using the MP2 method. After comparing four possible conformations, the most stable one was found, which has the typical hydrogen bonding feature of red-shift effect. Based on it, the substituent effects on both nitro-compounds and (thio) urea were researched. The results indicated that electron-withdrawing groups on ureas or thioureas and electron-donating groups on nitro-compounds can both facilitate the hydrogen bonding formation. The NBO analysis further disclosed the essence of the hydrogen bonding interaction. We also studied the cis-trans isomerization of the complexes of (thio) urea with nitroalkenes, which revealed that, for hydrogen-bonding complexes, it is necessary to take both cis and trans isomers into consideration, especially for nitroalkenes with little steric effect substituents.