Preheat the oven to 325 degrees Fahrenheit. Grease a 9-inch springform pan and line the bottom with parchment paper if desired.
In a medium bowl, combine graham cracker crumbs, melted butter, and sugar. Stir until evenly mixed and the crumbs resemble wet sand.
Press the mixture firmly into the bottom and slightly up the sides of the prepared pan using the bottom of a glass or measuring cup.
Bake for 10 minutes until lightly golden. Remove from the oven and cool completely.
Add chopped rhubarb, sugar, and lemon juice to a saucepan over medium heat. Cook while stirring often for 8 to 10 minutes until the rhubarb softens and thickens into a chunky sauce.
Remove from the heat and stir in vanilla extract. Allow the mixture to cool fully before using.
In a large mixing bowl, beat softened cream cheese until smooth and creamy with no lumps remaining.
Add sugar and continue mixing until fluffy and fully combined.
Add eggs one at a time, mixing slowly after each addition.
Mix in sour cream, vanilla extract, and flour until smooth and creamy. Avoid overmixing.
Pour half of the cheesecake batter over the cooled crust and smooth gently with a spatula.
Spoon part of the rhubarb filling across the batter in small dollops.
Add the remaining cheesecake batter on top, then spoon the remaining rhubarb mixture over the surface.
Use a knife or skewer to gently swirl the rhubarb into the cheesecake batter.
Place the cheesecake into the oven and bake for 55 to 70 minutes until the edges are set and the center still jiggles slightly.
Turn off the oven, crack the oven door open slightly, and let the cheesecake cool inside the oven for 1 hour.
Remove the cheesecake from the oven and cool completely at room temperature.
Cover tightly and refrigerate for at least 6 hours or overnight before slicing and serving.