Pickering emulsions stabilized with bioactive nanocrystals (BNC-PEs) have attracted increasing attentions in recent years. However, the mechanisms for the construction of stable BNC-PEs remain obscure. This study aimed to investigate the effects of the bioactive molecular structure and the initial pH of the aqueous phase on the fabrication and stability of BNC-PEs and the crosstalk between the two factors. Puerarin, tanshinone IIA and ferulic acid with unique structural characteristics were employed as model components to prepare BNC-PEs. Results showed that the initial pH of the aqueous phase significantly affected the stability of BNC-PEs through influencing the particle sizes and charges of nanocrystals, while the molecular structure of bioactive substances affected the three-phase contact angles or interfacial tensions. The construction and stability of the three kinds of BNC-PEs were all improved with increasing initial pH of the aqueous phase. Moreover, it was first found that the bioactive molecular structure strongly interfered with the influences of the initial pH of the aqueous phase on the stability of BNC-PEs. This study demonstrated for the first time that there might be a crosstalk between the bioactive molecular structure and the initial pH of the aqueous phase, and that the optimal pH of the aqueous phase might be intricately linked to the molecular structure of bioactive nanocrystals for BNC-PEs.