For magmatic rocks, it is often found that zircon 206Pb/238U and 207Pb/235U ratios continuously plot on the concordia line with a relatively large age span for the same sample, which gives rise to large dating errors or even unrealistic dating results. As the trace element concentrations of zircon can reflect its equilibrated magma characteristics, they can be used to determine whether all the analytical spots on the zircons selected to calculate the weighted mean age are cogenetic and formed in a single magma chamber. This work utilizes the results of zircon trace element concentrations and U-Pb isotopic analyses to explore the screening of reasonable U-Pb ages, which can be used to determine a more accurate intrusion crystallization age. The late Mesozoic Huayuangong granitic pluton complex, which is located in the Lower Yangtze region, eastern China, was selected for a case study. The Huayuangong pluton comprises the central intrusion and the marginal intrusion. Two samples from the marginal intrusion yielded consistent zircon weighted mean 206Pb/238U ages of 124.6 ± 2.0 Ma and 125.9 ± 1.6 Ma. These analytical spots also exhibit Zr/Hf and Th/U ratios concordant with the evolution of a single magma, from which the dated zircons crystallized. However, for the central intrusion, the analytical spots on zircons from two samples all show a continuous distribution on the concordia line with a relatively large age span. For each sample from the central intrusion, the zircon Zr/Hf ratios do not conform to a single magma evolutionary trend, but rather can be divided into two groups. We propose that zircon Zr/Hf ratios can provide a new constraint on U-Pb zircon dating and zircon Th/U ratios can also be used as a supplementary indicator to constrain zircon dating and determine the origins of the zircons and whether magma mixing has occurred. By screening zircon analytical spots using these two indicators, the two samples from the central intrusion of the Huayuangong pluton produce results of 122.8 ± 4.3 Ma and 122.9 ± 2.2 Ma, which are consistent with the field observations that the central intrusion is slightly younger than the marginal intrusion.