Hypospadias is a condition where the meatus(penis hole) isn't at the tip of the penis. Instead, the hole may be any place along the underside of the penis. The meatus (hole) is most often found near the end of the penis ("distal" position). But it may also be found from the middle of the penile shaft to the base of the penis, or even within the scrotum ("proximal" positions). Over 80% of boys with this health issue have distal hypospadias. Hypospadias is a common birth defect found in up to 1 in every 200 boy. In most cases, hypospadias is the only developmental problem in these infants and doesn't imply there are other flaws in the urinary system or other organs

See a Paediatric Endocrinologist. The penis has to be measured first to confirm if really small and if truly he has micropenis the child will be evaluated for the possible causes and treatment