Objectives: This study investigates the correlation of critical factors influencing throughput and efficiency in diffusion-based molecular communication systems. Method: The study presents a simulation model for 3-D diffusion-based molecular communication, incorporating essential parameters such as molecule size, transmission rate, diffusion rate, and transmitter-receiver distance. Findings: Through comprehensive simulations, the study reveals the effects of different parameters on throughput and efficiency in diffusion-based molecular communication. It highlights the critical trade-offs associated with system design and optimization. The study reveals the key factors influencing the transmission capabilities, the receiver congestion, and the overall efficiency of the communication system. Novelty: In this study, we give a study overview of the latest work of performance metrics in the field of molecular communication. A novel algorithm is proposed to find the throughput and efficiency of molecular communication. The proposed framework analyzes the intricate relationship between system parameters and performance metrics, emphasizing the potential for system optimization. Our simulation work demonstrates how the model parameters influence the performance of the molecular communication system, providing insights for enhancing the system's performance in applications such as targeted drug delivery in the future. Keywords: Molecular Communication, Diffusion, Transmission Rate, Throughput, Efficiency