In this study, new specific compatibilizing agents based on phosphonium ionic liquids have been used in order to prepare high performance PP/PA6 polymer blends, in particular with excellent thermal and mechanical properties. The incorporation of only 1 wt% of trihexyltetradecylphosphonium bis(trifluoromethylsulfonyl)imide named as IL-TFSI and trihexyltetradecylphosphonium bis 2,4,4-(trimethylpentyl)phosphinate designated as IL-TMP in polypropylene/polyamide 6 (80/20 wt/wt) blends generated decrease in the size of the dispersed phase i.e. PA6. In fact, the size of the PA6 domains decreased from 27 to 1–2 μm. This reduction is attributed to the migration preferentially of ionic liquid at the interphase between PP and PA6 which creates a barrier around the PA6 drops, preventing their coalescence. In addition, the chemical nature of the counter anion has been demonstrated on the final properties of PP/PA6 blends. Thus, the use of ionic liquid combined with phosphinate anion (IL-TMP) results in a significant increase in strain at break of 1400% without reducing the Young’s Modulus while the ionic liquid with the ionic fluorinated anion (IL-TFSI) has a plasticizer effect characterized by an increase in elongation at break and a drop of Young’s modulus (−30%). Then, the addition of ionic liquid also causes an increase in the thermal stability of polymer blends: +20 °C for 1 wt% of IL-TFSI and +35 °C for IL-TMP. Nevertheless, an increase in the amount of ionic liquid leads to two different behaviors due to the distribution i.e. to the affinity of the counter anion with the polypropylene or polyamide 6 matrices. In fact, the more hydrophilic IL (IL-TMP) has a better affinity with the PA matrix while the hydrophobic salt (IL-TFSI) has a preference with the PP matrix which leads to a degradation of the final properties, especially for a large amount of IL used.