One of the prediction method of the long-term settlement of soft clay is to predict it by defining the linear slope of the latter half of the s-log t curve, as the rate of secondary consolidation. This method has some disadvantages, because the slope of the straight line is depending on how to set the origin of elapsed logarithmic time, and how to determine the initial thickness of soil layer, and so on. The author carried out a series of laboratory experiments using oedometer apparatus against some kinds of highly organic soil and one silty clay which were sampled in Japan. From the experimental results, the author proposed a prediction method for long-term settlement of highly organic soil based on the isotache theory using natural strain which can be used conveniently by eliminating previous problems. To confirm the applicability of the proposed prediction method, some field measurement data were used, constructed in Japan. They were good correlations, and the applicability of proposed method was proved in this study.