This study presents a comprehensive analysis of the combustion chamber characteristics of a variable compression ratio compression ignition engine powered with microalgae biodiesel/diesel and their impact on engine performance and emissions. Both numerical and experimental methods have been employed to study the problem. A computational fluid dynamics method is used to study the axisymmetric flow in the cylindrical combustion chamber. Numerical simulations are obtained by solving time-independent steady, incompressible Navier-Stokes equation in a two-dimensional cylindrical coordinate system. Fluid flow characteristics, such as velocity vector field, streamlines, and pressure distribution are presented for different biodiesel blends. The velocity vector field analysis shows that biodiesel blends exhibit high velocities near the axisymmetric wall region. Swirl motion generated near the outer periphery of the combustion chamber influences the flow patterns. The experimental study involves the engine performance and its emissions. Due to the increase of biodiesel blend ratios in B20 (20% biodiesel and 80% diesel), B40 (40% biodiesel and 60% diesel), B50 (50% biodiesel and 50% diesel), and B100 (100% biodiesel), the brake thermal efficiency (BTE) decreases for a given brake power. B20, B100, and diesel exhibit 32.87%, 29.15%, and 34.45% BTE respectively. Higher brake-specific fuel consumption is obtained at no-load engine operations due to incomplete combustion of fuel. B20, B40, B50, and B100 show reductions of 16.04%, 20.85%, 25.66%, and 32.08% CO, respectively, as compared to diesel. HC emissions are very low for all biodiesel blends, while B20 exhibits a decrease of 7.35% HC compared to diesel. However, NOx emissions increase with the biodiesel blend ratio, with B100 exhibiting a 22.56% increase in NOx compared to diesel. Smoke emissions decrease with an increase in the biodiesel blend ratio, while B20 shows a 4.64% reduction. Results show that B20 offers a favorable balance between emissions reduction and engine performance. This study determines the biodiesel combustion characteristics and insights for the practical implementation of biodiesel blends in the transportation and energy sectors.