The muddy soft soil under the miscellaneous fill foundation can easily be squeezed into the pores between the miscellaneous fill particles under the action of the overlying load, causing mutual settlement. This part of the settlement is not considered in traditional foundation settlement calculation methods. Using a self-developed soil intercalation experimental instrument, one-time loading, conventional graded loading, and composite multi-stage loading tests were conducted on soft soil and miscellaneous fill in the Qinhuai River area of Nanjing, revealing the development law of intercalation settlement under different loading methods. The results show that under different loading methods, the total settlement and embedded settlement show a stepwise growth trend, with a sudden increase in settlement at the moment of loading, then gradually slowing down and stabilizing. The difference in the total settlement and embedded settlement mainly comes from the settlement changes at the moment of load application. In the case of multi-level loading, the embedded settlement is negatively correlated with the loading order and positively correlated with the load proportion. Through curve fitting, it was found that the embedded settlement is logarithmically correlated with the loading order and exponentially correlated with the load proportion. The proportion of embedded settlement is negatively correlated with the loading order and positively correlated with the proportion of load. Moreover, when the particle size is large, the sensitivity of the embedded settlement proportion to the loading method decreases.