The invention relates to a silicon-based rhodamine derivative, which is represented by a biological structural formula shown in the description. The invention also relates to a preparation method of the silicon-based rhodamine derivative, and applications of the silicon-based rhodamine derivative in preparation of cell dye, biological dye, biological molecule / particle fluorescent marker, and the like. The provided synthesis method of silicon-based rhodamine derivative has the advantages of high yield, simple reaction conditions, convenient operation, capability for massive production, and wide substrate selection range.