With the ability of sensing the electromagnetic environment, the Transform Domain Communication System (TDCS) can avoid jamming, with an excellent performance of anti-jamming. The base function generation is the core in the algorithms of TDCS. After an analysis od shortcomings of existing algorithms for base function generation, an algorithm of using adaptive multi-threshold in the base function generation is proposed in the paper for the TDCS. The algorithm uses a multi-structure, making the traditional adjudicate result more refined to reflect the difference of channel quality more accurately, based on the traditional binary adjudicate. The theoretical analysis shows that the algorithm of generating base functions based on adaptive multi-threshold can overcome the shortcoming of the traditional threshold estimation algorithm of bad adaptability with respect to channel circumstance. And the threshold design of the algorithm is simple, with good interference suppression performance.