Here, the high fluorescent silicon-doped carbon quantum dots (Si-CQDs) were prepared by a facile and one-pot hydrothermal assay using 3-aminopropyltrimethoxysilane as the carbon and silicon source. The prepared Si-CQDs exhibit favorable water-soluble, high-temperature resistance, acid resistance, alkali resistance, high ionic strength resistance, high photostability, film-forming ability and solid-state fluorescence. Compared to other Si-CQDs that have been reported, the prepared Si-CQDs show unique up-conversion fluorescence. Furthermore, it is found that berberine hydrochloride (BH) can effectively quench the down- and up-conversion fluorescence of the Si-CQDs, making it can be used as a highly sensitive and specific probe for BH dual-mode sensing. Meanwhile, the linear range of down-conversion fluorescence detection for BH is 0.5-30.0 µmol/L with a limit of detection (LOD) of 50 nmol/L, and the linear range of up-conversion fluorescence assay for BH is 0-25.0 µmol/L. The mechanism of down-conversion fluorescence quenching by BH was investigated through a series of studies. The results show the quenching mechanism is the inner filter effect (IFE). Moreover, this proposed strategy has been well used to analyze BH in urine samples with satisfactory results.