Two novel metal-organic frameworks (MOFs), HBNU-1 and HBNU-2, have been synthesized successfully. We adopt a step-by-step assembly strategy, which first synthesize the Cu3 cluster Cu3(μ3-OH)(pz)3(CH3COO)2(Hpz), and then react it with H2BDC under different conditions to form final frameworks. In both MOF structures, the Cu3 clusters are maintained, although certain differences are observed. Compared with HBNU-1, the Cu3 cluster dimerizes into Cu6 cluster in HBNU-2. With this step-by-step cluster assembly strategy, MOF structure predicting becomes possible and may give some reference for MOF structure designing.