To address the sensor placement challenges in ultra-slender and flexible structures such as deep-sea mining risers, the traditional effective independence method (EI) is improved by using the modal strain energy coefficient and the strain modal energy coefficient in this paper. A stepwise optimization and recombination strategy is further employed to extend the method to the scenarios of multi-type sensor placement. Based on this approach, a numerical simulation of a 6000-meter-class riser is conducted to explore the placement schemes of acceleration and strain sensors in such scenarios. Finally, for the five candidate schemes, three types of criteria are proposed to evaluate and select the optimal configuration. The results demonstrate that a combination of 21 acceleration sensors and 24 strain sensors can achieve a relatively ideal layout effect, which can reduce the maximum value of off-diagonal elements in the MAC matrix to below 0.1. The relevant research conclusions can provide a theoretical reference for the engineering practice of optimizing the placement of deep-sea mining riser sensors.