Productive tiller percentage (PTP) is the only available comprehensive indicator of rice population quality. However, productive panicle number (PN) has a great effect on its characterization accuracy. Panicle exsertion is an important but difficult to describe morphological index; therefore, it cannot be easily determined. The aims of this study were to develop heading uniformity (HU), which describes the difference in the degree of rice panicle exsertion, as a new comprehensive indicator by designing a representative sampling and calculation method and exploring the relationship between HU and yield components. HU first decreased then increased after initial heading, exhibiting a single-valley curve. Adequate HU was obtained by panicle sampling on day two or three (panicle N fertilizer proportion ≤40 or >40%) after initial heading. The explanatory power of PTP for grain yield variance was markedly insufficient in low- and high-PN rice populations. Compared with the percent contribution of PTP to grain yield variance (12.32–41.26%), that of HU (49.02–61.93%) was greater and more stable across rice populations of different PNs. Moreover, HU showed fewer interannual variations, despite large interannual differences in weather and soil conditions. Hence, HU may have applications as a comprehensive indicator of rice population quality.
