Isabella has a huge crush on Phineas. She is usually seen hanging around with Phineas, and helping him with his daily activities. She always finds his ideas to be a lot of fun. Although she usually just speaks to him as a friend, she occasionally attempts to flirt with him and cutely greets him with the phrase "Whatcha doin'?" almost every time they first see each other each day.
Isabella gets very upset about the fact that Phineas rarely notices her. This has been shown many times, most noticably in the episodes The Chronicles of Meap where, when the two are searching for Meap, they use a "cute tracker", which keeps getting a cute interferance. Isabella is upset, when Phineas refuses to admit that Isabella may be causing the cute interferance. However, Isabella is happy when she finds out Phineas programmed the cute tracker to ignore her cuteness. Another episode where Isabella gets upset about Phineas not noticing her, is in the episode Summer Belongs to You, where when Isabella is singing to Phineas, he pays no attention to her.
It is unknown if Phineas has any feelings for her, but it has been hinted that he does. In the movie Phineas and Ferb Across the Second Dimension, at the end, before being hit by the "Amnesia-inator". Isabella asks Major Monogram if the machine would make them forget everything that happened that day, he assures her of it, and she kisses Phineas. Phineas smiles and says her name, sounding pleasantly surprised. She then tells Carl to "hit it", much to the dissatisfaction of Phineas, who proceeds to cry out, "Wait, wait, wait". This indicates that he wanted to remember this moment or to return his feelings for her, even if it were just for a moment.
In the episode, Phineas and Ferb Quantaum Boogaloo, Candace's future daughter states that Isabella looks like "Aunt Isabella". Thrilled, Isabella realized that she will marry into the Flynn-Fletcher family in 20 years and exclaimed to Candace that she must have married Phineas. However, Candace reminded her that she could have married Ferb, which sent Isabella into speechless shock
In the movie, Star Wars: Phineas and Ferb, Isabella kissed Phineas in the near end of the movie, leaving Phineas smiling dreamily. Also, they were seen dancing at the end of the movie in the song, Rebel Let's Go!
SPOILER (Do not read at your own risk.)
In the episode, "Act Your Age", him and Isabella grew into an adult. Baljeet, Buford, & Ferb said to him that Isabella fell in love with him since they were kids, leaving Phineas shocked. They also sang/have their duet. Isabella and Phineas kissed at the end of the episode.