The present 3‐D numerical paper investigates Nusselt number and friction factor variations in a capsule heat exchanger filled with eco‐friendly jatropha seed oil–based MWCNTs nanofluid. For all studied models, inlet nanofluid temperature is Tin = 310 K, and the hot source with q = 650 W/m2 is adopted. Due to achieve the most efficient Newtonian nanofluid in present study, solid nanoparticles of MWCNT are added to the base fluid in volume concentration of 0.2% to 0.8%. Also, different riser heights (25, 35, and 50 cm) and different emissivity values of capsule walls (ε = 0.3 and 0.7) are studied in this paper. In the current modeling, the SST k – ω turbulence model has been assumed as the turbulence model. Based on achieved results in this paper, the model with capsule angle of β = 30° has better heat transfer than the other studied slopes, which is followed with models with β = 60° and β = 90°, respectively. Also, it is seen that gravity has a significant influence on velocity contours, and in model with β = 90° more pressure drop may be seen, which is followed with models with β = 60° and β = 90°, respectively. Moreover the predicted pressure drop values from inlet to outlet always increase by increase of Reynolds numbers; therefore, there is an optimum Reynolds number during the studied range of flow velocities which leads to the minimum pressure drop penalty. Also, it is realized that usage of nanofluid at higher nanoparticles volume concentrations leads to higher Nusselt numbers during all studied Reynolds numbers. The model with nanoparticles volume fraction of ϕ = 0.8% has the highest values of predicted average Nusselt number which is followed with the models with ϕ = 0.6%, ϕ = 0.4%, and ϕ = 0.2%, respectively. Besides, it is clearly found that usage of walls with different emissivity values has not a significant influence on thermal–hydraulic characteristics of studied capsule heat exchanger.