New secondary building units (SBUs) in metal–organic frameworks (MOFs) open opportunities for the rational design of new MOF structures and their emerging properties. Zr-based MOFs are one of the representative classes of MOFs, featuring high chemical stability, various topological structures, and practical applications. Recently, the number of new Zr SBUs is rising, while the first type of Zr SBU (Zr6) has been exclusive for a long time. Several new Zr SBUs exhibit higher performance than that of Zr6 in catalytic and adsorptive properties. Before the discovery of several new Zr MOF SBUs, their molecular counterparts (Zr molecular clusters) have been reported. A survey on unlooked Zr molecular clusters unveils their diverse structural types. Understanding Zr molecular clusters will provide important clues to access future Zr-based MOFs. The predefined geometries of metal–organic framework (MOF) building blocks, which consist of secondary building units (SBUs) and organic linkers, are integral to the rational design of new structures. In contrast to that of organic linkers, access to new SBUs is a daunting challenge because of their complex chemistry during MOF synthesis. Here, we present novel opportunities for molecular clusters to bring future SBUs in MOF chemistry. This opinion article summarizes recently emerging structural types of Zr SBUs and provides an understanding of Zr molecular clusters, suggesting them as new SBU candidates. A structural library of Zr molecular clusters will accelerate the discovery of new Zr-based MOFs and motivate similar analysis on various classes of MOFs.