This paper explores the security vulnerabilities in Frequency Hopping (FH) signals within Integrated Sensing and Communication (ISAC) systems, focusing on the risks of eavesdropping and location privacy breaches due to FH sequence leakage. Unlike existing methods using Channel Reciprocity-based Key Generation (CRKG) at higher communication layers, this research pioneers a novel approach. CRKG is creatively applied to enhance security in the physical layer of FH signal transmission. Innovative strategies, including Multiple Input Multiple Output (MIMO)-FH modulation on FH sub-pulses and vector quantization, generate shared secrets as FH sequences, increasing entropy and randomness significantly. The study involves the embedding of information into MIMO-FH sub-pulses using Phase Shift Keying (PSK) modulation techniques, demon-strating superiority over traditional techniques with enhanced FH sequence similarity, higher entropy, randomness, and reduced Bit Error Rates (BER). These findings significantly advance the security and privacy of FH communication in ISAC applications.