Spatial averages have been widely used in scientific research and practical applications since they were proposed. How to estimate the weight coefficient in the spatial average has been a problem studied by many scholars. In the case of missing data, the spatial average is the ratio of the two random variables R = ∑ βi si ri as well as S = ∑ βi si . In this paper, we use the “ Delta method”to derive approximate formulas for the squared bias, variance, and mean squared error of the estimatorr used to estimate the true spatial average, assuming that the weight βi is known. The bias of the estimator r and the source of variance are analyzed, and the spatial average estimated weight to minimize the bias is given. Finally, the obtained results are applied to the global relative abundance data of ammoniating archaea.